A man is known by the company he keeps为什么是he keeps而不是his keeps

the company that he keeps
后面是定语从句，省略了that。
he在定语从句里面做主语，所以用主格

物以类聚 人以群分

还原过来是he keeps the company(他结识的人)
句中颠倒了一下

he keeps 是定语从句修饰the company ,he在从句中做主语,当然用主格

keep是动词呀 怎么能用形容词性物主代词？
是一个从句the xompany(that/which)he keeps

你可以这样理解，A man is known by the company (which/that ) he keeps.
所以不用his keep.一个人因他开的公司而被别人知道.这是定语从句，而且省略了定语代词。