Polymer microfluidic chips have high requirements for bonding precision, bonding strength and bonding efficiency. In order to avoid the clogging of microchannel by fusion and solve the problems of low bonding strength, uneven pressure distribution caused by leveling precision and high-frequency vibration in the process of ultrasonic bonding, the joint structure and self-balancing jig were designed and fabricated. First, based on the self-balancing jig and conventional jig with no leveling function, the pressure distribution coefficient was defined and measured by prescale film. Moreover, the chips we designed were bonded with two types of jigs respectively. The bonding line and cross-section of microchannels were measured by measuring microscope. Last, these chips were tested by electric tensile tester and sealing test. Experimental results indicate that the precision of controlling microchannel can reach about 2.0 μm. The self-balancing jig can improve pressure distribution about 35.20%-43.18% with simple structure and easy operation, and make the bonding line uniform. The bonding strength increases about15.3%-45.1% with excellent sealing performance. It concludes that the joint structure and self-balancing jig can satisfy the requirements of controlling precision, bonding strength, pressure distribution and sealing performance.