Inertial Navigation System (INS) is often combined with Global Navigation Satellite System (GNSS) to increase the positioning accuracy and continuity. In complex urban environments, GNSS/INS integrated systems suffer not only from dynamical model errors but also GNSS observation gross errors. However, it is hard to distinguish dynamical model errors from observation gross errors because the observation residuals are affected by both of them in a loosely-coupled integrated navigation system. In this research, an optimal Radial Basis Function (RBF) neural network-enhanced adaptive robust Kalman filter (KF) method is proposed to isolate and mitigate the influence of the two types of errors. In the proposed method, firstly a test statistic based on Mahalanobis distance is treated as judging index to achieve fault detection. Then, an optimal RBF neural network strategy is trained on-line by the optimality principle. The network’s output will bring benefits in recognizing the above two kinds of filtering fault and the system is able to choose a robust or adaptive Kalman filtering method autonomously. A field vehicle test in urban areas with a low-cost GNSS/INS integrated system indicates that two types of errors simulated in complex urban areas have been detected, distinguished and eliminated with the proposed scheme, success rate reached up to 92%. In particular, we also find that the novel neural network strategy can improve the overall position accuracy during GNSS signal short-term outages.