Two channels of photon arrivals are applied to construct fiber pseudo-random depth acquisition photon counting system. In order to find the method to diminish the depth error, Gauss function is used to model laser echo pulse. By calculating the probability density function,the time walk effect is introduced and the Cramer-Rao lower boundary is modeled. The theory model proves that with the growing signal energy, the depth error decreases sharply firstly and then rises and the longer code length can bring smaller depth error. From the theoretical part, using the cumulative distribution function to generate photon arrivals and simulate the pseudo-random depth acquisition photon counting system, Monte Carlo simulation results are larger than the numerical modelling,which agree with Cramer-Rao lower boundary. 17 experimental tests also converge to the presented boundary model in this paper. It has been proven that fluctuation of the number of detected photon counts in the laser echo pulse caused by different target reflection leads to the depth drift of Correlation Function on pseudo-random depth acquisition photon detection process. Finally, numerical fitting function is used to determine the relationship between the depth error and the photon counting ratio. Depth error is calibrated by substituting the measured photon counting ratio into numerical fitting function. The corrected depth RMSE is decreased to 1 cm.