Several new methods to improve the time accuracy and resolution based on the original X pulsar navigation ground simulation system are proposed. By these proposed methods, the accuracy and real-time performance of the spacecraft navigation has been enhanced. The methods adopted include: 1) enhancing the performance of the photon counting detector based on micro-channel plate (MCP); 2) using time measurement system with high accuracy. The pulse profile of the original detection system is compared with the pulse profile of the improved detection system, and the gain of MCP which has influence on the detected pulse profile is discussed. The experimental results show that the counting rate of improved detection system becomes higher under the same experimental condition. When the operating voltage of MCP is -800 V in the improved detection system, and the value of Bin is 1.5 ms, a pulse profile with good signal-to-noise ratio (SNR) can be acquired after being integrated for 200 s.