In this paper, the digital model of the micro-factory has been established, inspected and evaluated by progress of assembly, manipulation and examination. The new paradigm of the system analysis is realized by digital simulation of the factory. The digital manufacturing system of the micro-factory was simulated through UML(Unified Modeling Language) with the object-oriented logical model analysis method and then the micro lens module assembly system was simulated with MST(Micro System Technology) Application Module.