I met a problem that I custom a post type for all user in the wordpress system. and the post type is a many-to-many relationship of user.
Can I make the relationship between My Custom post Type and User??
You can't do that directly. We will be adding support for this in a future release but for now you have to rely on workarounds. You can create a custom post type that has a one-to-one relationship with users, you could call it Profile. From the you can follow the normal procedure for many to many relationships.
Lets say your Profile custom post type has a "user_id" field to connect it to the user. To create a Profile for each user you can add these lines to functions.php in your theme: