According to the demands of an array detector in the X-ray pulsar navigation system for Micro-channel Plate(MCP), a selection method for the MCP was explored. Four key parameters for the selection of MCPs, the uniformity of gain, impedance matching, dark count rate and the gain coefficient were determined. Based on the four key parameters, corresponding experiments were designed and the selection process of MCPs was set out. The amplitudes and counting rates of MCPs selected by proposed method were tested. The tested results show that the relative error of each detection unit is not identical. When a single channel anode is used, the ranges of the maximum relative error Δ1i and minimum relative error Δ2i of the amplitudes for output signals from the ith anode are 7%-13.5% and 3%-6.7%, respectively, and when a four-channel anode is used, Δ1i and Δ2i are 7.8% and 3.1%, respectively. Moreover, the relative error between the anode count rate n1+n2+n3+n4 from the single channel and N from the four-channel shared anode is 4.38%, less than 10%. Obtained results indicate that the MCPs with good performance have been effectively chosen by the proposed selection method.