Based on the merger design theory, the transportation of the merger in PKU-ERL is designed,and the optimized parameters is given which can satisfy the demands of PKU-ERL. The increasements of the emittance and energy spread caused by space charge and coherent synchrotron radiation(CSR) in the merger part are studied. Simulation results show that space charge influences the beam envelope obviously but has little influences on the emittance. CSR has little influence on the emittance, the energy spread and the envelope.