Innovation design is a process that makes it easily to satisfy individual customer demands. This study is aimed to realize the innovation design of complex equipment with better satisfaction to the individual customer needs. Firstly, the optimization mathematical model of innovation design was established. Secondly, structural repository of multi-granularity was developed to support innovation design. Finally, in the application of the design of hydro cylinder of injection molding equipment, we demonstrated that our method successfully generated new designs with optimal design lifetime.