GPS signals are easily blocked and disturbed in urban canyons, resulting in the degraded accuracy, continuity and reliability of the navigation performance. In order to deal with the issue a GPS/IMU integrated navigation algorithm based on the geometric dilution precision (GDOP) and non-holonomic constraints (NHC) is proposed. As GDOP is able to evaluate the geometry of the constellation and positioning accuracy, a measurement update strategy of the GPS/IMU integration using GDOP is proposed. In addition, the NHC based constraint is applied in the integration. The experimental results show that for the proposed method, the root mean square errors of horizontal and 3D positioning results are 3.88 m and 4.78 m respectively, which are 58.06% and 64.67% higher than the 9.25 m and 13.53 m of the traditional GPS/IMU integrated navigation method respectively. The proposed method can effectively improve the positioning accuracy and reliability of integrated navigation system in the urban areas.