In order to assess the performance of detection system for X-ray pulsar navigation, the expression of the signal-to-noise ratio (SNR) and the minimum detectable power are derived in the photon counting mode of the system. Experiment system to measure the SNR and the minimum detectable power is setup. The minimum detectable power is measured; the SNRs at different integration time, optical power and threshold voltage are calculated. The X-ray pulse profile is reconstructed by measuring the time of arrival (TOA) of the X-ray photons. Experimental results show that the SNR of the pulse profile is improved and the curve of the pulse profile tends to smooth with the increasing of optical power and the integration time; the SNR is 26.3 and the pulse profile is optimal when the threshold voltage is -150 mV; the minimum detectable power of the system is 3.5×10-16 W.