The subnanosecond time resolution readout system includes a time discriminator module and a TDC module is designed for reading the signals detected by the MCP from the X-ray pulsar. The periodicity of the signals from the specific pulsar will be detected under a high background level with this system. Through the delay chain designed in the FPGA, the time accuracy of this TDC module is able to reach less than 500ps. To keep in line with the time resolution of the TDC, the jitter of the time discriminator module need to be designed less than 500ps. Through a special design with the chips ADCMP580 and NB7V52M, the time resolution required by pulsar-based navigation could be finally achieved by this readout system.