The meaning may change depending on the contexts.
But in general, It means he knows his own way of doing things.
For example, - 'Can he find where we are?
''Oh yes, he's lived here for long time. He knows his way'''
In this case, knowing the way literally means he knows the direction.
"Can your friend really fix my car?"
"Yes. He's worked as a mechanic before. He knows his ways. Don't worry".
Here, it'd mean he knows 'how to fix the car'. He knows how it can be done.