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Experiments are used to study the fabrication of polymer microfluidic chip with hot embossing method. The patt fidelity with respect to the process parameters is analyzed. Experiment results show that the relationship between the imprint temperature and the microchannel width is approximately exponential. However, the depth of micro channel isn’t sensitive to the imprint temperature. When the imprint pressure is larger than 1 MPa and the imprint time is longer than 2 min, the increasing of imprint pressure and holding time has little impact on the microchannel width. So over long holding time is not needed in hot embossing. Based on the experiment analysis, a series of optimization process parameters is obtained and a fine microfluidic chip is fabricated. The electrophoresis separation experiment are used to verify the microfluidic chip performance after bonding. The results show that 100bp-ladder DNA sample can be separated in less than 5 min successfully.