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Bonding is an essential step to enclose microchannels or microchambers in lab-on-a-chip. Ultrasonic bonding was studied as a deformation-free technique to realize high efficiency bonding of microfluidic chips. Based on viscoelastic dissipation theory, the main influential factors of heat generation rate during ultrasonic bonding was theoretically analyzed and numerically calculated using finite element method. According to the results, micro energy directors were designed to concentrate the ultrasonic power and to control the location of the joint. To demonstrate the performance of this bonding method, specially designed PMMA substrates of microfluidic chips were fabricated by means of hot embossing. With the ultrasonic bonding technique, the chips were reliably and hermetically bonded within less than a second.