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In order to meet the requirements of MEMCAD development, realization method for dynamic analysis and optimal synthesis for micro-components (DAOPMC) was studied in this paper. There, the finite element method (FEM) was used to analyze the dynamic properties of coupled-energy-domain of virtual prototype instances and obtain the optimization data, the rough set theory (RST) and the genetic algorithm (GA) were used to dispose the data to confirm key variable and restriction condition in the synthesis optimization, based above information obtained, the regression analysis (RA) and GA were used to establish the synthesis optimization model. Finally, the intelligent prototype system of (DAOPMC) was developed based on IDSS, JAVA, SQL, PRO/E and ANSYS etc. and the dynamic analysis and optimal synthesis of a thermal actuated micro-pump was carried out as a demonstration in this paper.