It is impossible to be sure about what prehistoric peoples knew about the workings of the body. But we can make some good guesses, based on the little bits of information we do have.

Engraving by William Blake of an Aboriginal family from New South Wales, Australia
If we assume that prehistoric peoples were similar to the few remaining primitive peoples of the modern age, we can also assume they knew little about the inner workings of the body.
Some of their burial practices (where bones were stripped of the flesh, bleached and buried in different piles), however, suggest that they must have known at least something about bone structure. And archaeologists have found evidence of cannibalism amongst some prehistoric people, so presumably these people also knew something about the flesh and inner organs of the body.
It is possible that prehistoric people believed that life and the functions of the body were determined by the spirits ('animism'). The Australian Aborigines of recent times believed that illness occurred when a person's spirit was lost or stolen by an enemy.
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