In order to use a micro ultrasonic bonding method to package polymer microfluidic chips,an auxiliary microstructure named micro energy director is designed and fabricated on two sides of the microchannel by a selective bonding method in this paper. A hot embossing method is adopted to fabricate this newly designed Polymethyl Methacrylate(PMMA) substrate containing both convex micro energy directors and concave microchannels,then a complex silicon mold is designed and fabricated by the multi-photolithography and wet etching. By the Taguchi method,the optimized parameters for hot embossing are obtained. Experimental results show that the optimized embossing temperature is 15-20 ℃ higher than that of the simply replicate concave microstructure,since concave and convex micro structures are formed simultaneously. With the optimized parameters in an embossing temperature of 140 ℃,holding time of 300 s,and an embossing pressure of 1.65 MPa,the accuracy of replication can be up to 99%.