Abstract: Residual stress exists in the PMMA microfludic chip due to the different thermal expansion coefficience,also called thermal mismatching of the mold and the polymer,which can result in the warpage and deformation of the chip.In this paper experiment method was mainly used to study on the residual stress of the chip during the hot embossing,the process parameters including temperature time and pressure affecting the residual stress have been analysed and optimum parameters minimizing the residual stress have been decided,meanwhile it has been confirmed that temperature difference of about 10℃ can greatly reduce the warpage and deformation of the chip.Finally finite element analysis method was utilized to test the experiment results.