The superiority of a global navigation satellite system (GNSS)/inertial navigation system (INS) ultra-tight integration navigation system has been widely verified. For those systems with centralized structure based on coherent-accumulation measurements (I/Q), the conversion from I/Q signals to navigation information is implemented by an observation equation. As a result, the model is highly complex and nonlinear, exerting essential influence on system performance. Based on the analysis of previous studies, a novel model and its linearization method are proposed, aiming at the integrity, stability and implicit nonlinear factors. Unlike the one-order precision in the common Jacobian matrix, two-order components are partly reserved in this model, which makes it possible for higher positioning accuracy and better convergence. For the positioning errors caused by ignoring code-loop deviation, a method to approximate code-phase is proposed without introducing new measurements. Consequently, the effect of code error can be significantly reduced, especially when the tracking loops are unstable. In the end, using real-sampled satellite signals, semi-physical experiments are carried out and the effectiveness and superiority of new methods are proved.