As a stacked form of ultrathin polymer films, multilayer nanostructures are of great interest in various applications. Coarse-grained molecular dynamics simulations were carried out to understand the behaviors of interfacial diffusion and bonding of multilayer polymer films. We found two obvious stages for the interfacial diffusion of polymers in the multilayer film, and it is 3 times faster in the first stage than in the second one due to the evolution of molecular conformations. The polymers near the interfaces have an in-plane mobility much higher than the out-of-plane one. The strength of interfacial bonding has been characterized by the fast tensile stress-strain curve along the normal direction. It shows multiple yielding points for the multilayer polymer films, which is distinct from the tensile behavior of the bulk. The ultimate tensile stress (UTS) and corresponding separating strain, surprisingly, do not necessarily increase with diffusion time. Because of the dramatic molecular rotation and extension during the first stage of interfacial diffusion, the interlayer interpenetration is nonuniformly distributed in the plane of the interface. Such a nonuniform distribution may be one of the reasons for the decrease of the UTS and separating strain.