I had already registered the permission in this way:

PermissionAPI.registerNode("permission", DefaultPermissionLevel.OP, "permission");

And how to set players' permission?

Forge's PermissionAPI is pretty basic, it only allows a framework for others to build upon. The PermissionAPI has a IPermissionHandler object it reroutes things to. The handler is the object that decides what to do. By default forge uses a DefaultPermissionHandler as it's handler. It's implementation allows all players for permission level of ALL, denies all players for a level of NONE and if the level isn't either of those it simply checks whether the player can send commands or not. 

As you can see the default implementation doesn't allow you to have permission levels per player per se - it just checks whether the player is allowed to use commands or not.

You need to find an API that actually expands upon forge's permission API.