The equivalent problem of the code tracking bias introduced by generalized joint channel and the overlaying value of each part of the channel were researched. The influence of the code tracking bias caused by the channel characteristics of satellite-ground joint channel and each part of the channel was studied. The possible causes of pseudorange layered in the actual channel were analyzed. The nonideal characteristics of the channel affected the tracking performance of the navigation signal. The pseudo code tracking function and channel characteristics were modeled the non-ideal characteristics of both the satellite channel and the receiver channel were considered. The influence of different channel characteristics on code tracking bias was analyzed. Simulation verification was carried out with a software receiver. By analyzing the influence of several typical channels on pseudorange error, this research explains the causes of pseudorange layered phenomenon in the double-difference observation of zero-base line. Test results in practical channels prove the correctness of the analysis model. The model and analysis method can be used to explain signal quality problems and guide the optimal design of receiver channel.