With the rapid development of safety critical applications of Intelligent Transportation Systems (ITS), Global Navigation Satellite System (GNSS) fault detection and exclusion (FDE) methods have made navigation systems increasingly reliable.However, in multi-fault scenarios of urban environments, FDE methods generally demand massive calculations and have a high risk of missed detection and false alarm.To deal with this issue, we proposed a factor set based FDE algorithm for the integration of GNSS and Inertial Measurement Units (IMU). The FDE is first performed efficiently via consistency checking over far fewer subsets of the pseudorange. Afterwards, the FDE results are validated by missed-detection and false-alarm checks. The misseddetection-check factor is designed by predicting the maximum horizontal GNSS positioning error, while the false-alarm-check factor is designed with the aid of IMU mechanization. Following FDE, a loosely coupled GNSS/IMU integration is carried out to output the final estimation of the position, velocity and attitude of the vehicle.The proposed algorithm improved both horizontal and 3D positioning accuracy by more than 50% in the field test, compared to the traditional GNSS/IMU loosely coupled scheme. Additionally, with the proposed algorithm, the resultant accuracy of the velocity and of the heading angle were improved by over 20% and 50% respectively.