- This is more or less accepted canon; the film doesn't make any sense without this interpretation.
Kristen Wiig's character represents organized religionShe's essentially the same person as the Grand Inquisitor from The Brothers Karamazov. Even though her relationship with Him is a business relationship, Him inappropriately puts her ahead of his marriage to Mother (reflecting the description of the Church as the "bride of Christ"). She's the one who brings his work to the masses, who encourages them to crowd around him for photographs and memorabilia, and who, once everything goes to Hell, becomes some kind of tyrant gleefully executing prisoners. (Note that in her credits her title is given as the religious-sounding "Herald".)
The repeated cycle of Him's wives destroying the house represent real-life planetary extinction events.His first wife, 2.45 billion years ago, set off the Great Oxygenation Event and murdered all the houseguests, who were anaerobic life forms. This has repeated five times since then, killing ungrateful and decadent trilobites, giant crocodiles, etc. The woman we see at the beginning of the film is Cretaceous Mother, who has just vengefully wiped out the dinosaurs. The film we see is the tale of the Anthropocene Extinction, through a biblical lens, with the ending most likely a nuclear war. The ending of the film has New Mother awaken just as the Earth is recolonized by mutant cockroaches or self-aware nanotech or whatever, who now get their turn to prove if they can sustainably survive into the future.
Mother is Lilith.Or, in a gender reversal, perhaps Him is Lilith and Mother is Adam. Either way, the arc of the film is about the Curse of Lilith, the evolution of Lilith's brood into diverse sentient beings. Mother keeps wanting to undo this process, to be alone and being peace and quiet back to her house; Him disagrees, addicted to the mob of individual minds, each with "their own stories, their own point of view." The ending is Mother winning the argument and imposing Instrumentality.
Him is God and the Devil mixed into one.Him has hundreds (possibly millions) of devoted followers, who will support Him no matter and take his word for everything, even if it might be terrible. His fans as seen in this movie aren't just modern day Christians like most are, but the crazy fundamentalists who take everything he says word for word. While wanting to create the good in the world, Him is also responsible for all the evil in the world, such as the abuse of Mother (Nature), the abuse of the house (planet Earth), and all of the evil acts that human beings commit. The fact that Him takes and takes from Mother shows his abusive side as well.
Him represents domestic violence.Not only does Him allow for others to abuse Mother, but he does so himself as well, especially in the emotional form. Mother herself says this in the end, "you don't love me. You only love how much I love you." Because of Mother's undying love for Him despite his abuse (as many domestic abuse victims go through, standing by their partner), she agrees to let him destroy her completely in the end, even taking her heart away, so Him can start over again and move onto another victim. Their age difference is also apparent (and mentioned as well), as Him picks on young, vulnerable, naive women that he can easily manipulate, eventually replacing her with the younger lookalike model so he can repeat his cycle of abuse all over again.
Mother's house is the House of LeavesIt's a Bigger on the Inside structure that simultaneously represents a normal domestic household and contains the entire world. It is catastrophically destroyed only to later reappear. It even manifests in Will Navidson's life when his marriage is on the rocks due to his obsession with his artistic career.
The Extremely Short Timespan of the film is a dig at creationismOr, at least, at the extremely human-centric view of the universe religion provides. When Him puts the Crystal on the pedestal he summons the house and mother into existence in a matter of seconds, just as the creation myth of Genesis compresses billions of years of the universe's history into one week. Mother and the house seem to have memories of their history built into them, including remembering months of hard labor reconstructing the house piece by piece, that from our POV never happened — much like a religious point of view presumes the universe sprang into being with fossils already underground and starlight "on its way here", or, at the very least, treats all of that time before recorded human history as though it simply doesn't matter. Man and Woman have a whole backstory — they're indeed much older than Him or mother's apparent age and have two adult sons — that similarly took place in a dreamy parallel-universe past to the past we see where the universe was created this morning. Just like real human prehistory goes back far before The Bible and the creation myths therein. None of that implied history matters — for the movie's purposes mother's life begins on the day Man shows up at her house to see Him, just as from a religious perspective the story of the world begins with the first encounter between mankind and God/the gods.
The Binding of Isaac is an alternate ending to this film.In this timeline, Him finally gives in to mother's demands to kick out the houseguests to protect their son, but leaves with them rather than stick around in the "suffocating" house. Mother is Driven to Madness by his abandonment, alternately doting on and abusing her son until the events of the game. Notably, the Creepy Basement leading to some kind of hidden cave system is a dead ringer for the one in the game, and the "library" rooms in the game are a good match for Him's study.