The present inventions relates to a method for manufacturing a multilayer FPCB having different number of layers in different areas. The method includes the steps of: providing a binder layer; removing a portion of the binder layer thereby defining an opening in the binder layer; forming a multilayer FPCB which having a first copper clad laminate structure and a second copper clad laminate structure disposed on two opposite sides of the binder layer respectively using the binder layer; cutting the first copper clad laminate structure; cutting the multilayer FPCB in manner that a portion of first copper clad laminate structure that is exposed to the opening is separated from the first copper clad structure thereby obtain a multilayer FPCB having different number of layers in different areas.