In the story, the man (a marooned astronaut on an alien planet, perhaps) is living inside a sealed cave. The cave is sentient, and speaks to the man, and even provides food and water.
There's a weird scene where the cave wants to "become pregnant", and the only way for that to happen is for the man to use a knife to rip into a membrane in the cave... but there's danger involved, because the process (as with a black widow spider) involves the death of the one doing the membrane-shredding. The sentient cave somehow overcomes the instinct to kill the man, who has become her friend.
It was a bizarre story, probably from one of those Best Of ...." Books from the old Science Fiction Book Club.
Answer
This is Mother by Philip José Farmer, first published in 1953. Its page on ISFDB lists several places where it has been published since then.
Details are fuzzy (it's been 30 or 35 years since I read it) but here's what I remember:
The "cave" is the adult form of the planet's native life-form; as adults they are (mostly, as I recall) immobile and resemble large boulders; the juveniles are mobile and resemble snails. The parent captures prey, which fertilizes her by tearing the membrane that you remembered, before being digested. The young are grown inside the cave, and get expelled when they are old enough to survive. While inside the cave, the parent feeds them a "stew" of partially digested food.
There are a mother and son exploring the planet: the mother is a scientist studying the planet's biology, the son is a sulky brat. The son gets captured by one of the aliens and learns to cooperate with his captor as you describe (I think the aliens used radio to communicate).
At the end, the alien learns to produce food that the man can digest by:
capturing and killing his mother. If I remember right, there is a line in the story of him saying:
"Mother always did make great stew."
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