Queue length is one of the important indexes to evaluate the operation efficiency of signalized intersection and also the key parameter of intersection signal control optimization. Traditional queue length estimation models are mostly based on fixed detection equipment, and the models assumptions are too harsh; there are certain limitations. Based on the probe vehicle data, this paper establishes a model of queue length estimation for signalized intersection based on shockwave theory. First, based on the speed and location data of the probe vehicle, the vehicle density is calculated to estimate the intersection stop line. A real-time calculation method of vehicle arrival rate is proposed to improve the applicability of the model. Then, based on the shockwave theory, the meeting time of the queue forming wave and the queue discharging wave are calculated after the green light is on. Finally, the queue length is summed in sections, including the distance between the last queued probe vehicle and the stop line during the red light period, the length of the subsequent vehicles arriving during the residual red light time, and the newly increased queue length within the queue discharging time. This paper uses the VISSIM software to simulate the actual intersection. The simulation results show that when the penetration of probe vehicle is 50%, 25%, and 10%, their corresponding mean absolute relative error are 11.27%, 27.77%, and 39.12%, respectively. It can be seen that with the increase of penetration, the error gradually decreases. The average absolute relative error is within the acceptable range. After analyzing the existing similar methods, although the accuracy of the method proposed in this paper does not reach the highest level, it has the advantages of simple operation, less computation, and good real-time computation. Relevant research results can provide support for traffic control at signalized intersections.