Microchannel deformation is a problem which often occurs in the thermal bonding of polymer microfluidic chip, and which is significantly determined by bonding parameters. In this paper, numerical analysis of the microchannel deformation in the process of in-mold bonding polymer chip was conducted, using Young's modulus and shear relaxation modulus of polymethylmethacrylate (PMMA) obtained in creep tests. Adhesion between the top and two lateral walls of microchannel was observed in the results, which can be attributed mainly to the viscoelastic deformation of PMMA. It was also revealed that the maximum percent deformation of microchannel is in height, and that bonding temperature had greater effect on the deformation of microchannel than bonding pressure and bonding time. The deformation of microchannel in simulation were consistent with those of experiment under the optimized parameters of 105 °C, 2 MPa and 240 s.