The estimation of system accuracy is an important part in designing the satellite navigation system and a major indicator in assigning the large-scale system as well. Thus, much attention should be paid to simulating, computing and analyzing characteristics of all the error sources and their influences on system accuracy in designing satellite navigation system. This paper induces the covariance estimating expression of system positioning accuracy by differentiating the measure equations and the set of theory and method for controlling the critical error sources, which apply to engineering, is provided.