With the rapid development of railway construction, the mileage of railway detection has increased dramatically, and railway companies have higher requirements for the repeatability and accuracy of track geometric dynamic detection data. Therefore, the track geometry detection system needs to be calibrated to improve the measurement accuracy to ensure the safety of railway operation. However, the existing calibration methods of the track geometry detection system can only realize the static calibration and lack the dynamic calibration method, which cannot calibrate the track geometry detection system under the real operation state. Therefore, a dynamic calibration method for the track geometry detection system is proposed in this paper. A real and reliable test environment is provided for the track geometry detection system by presetting the track geometry irregularity and laying the rail dynamic displacement monitoring system on the calibration test line, and the dynamic and static differences of the track are analyzed based on the test environment. Based on the bisection method, this paper reduces the measurement error of the track geometry detection system and analyzes the measurement repeatability of the track geometry detection system. Finally, the error correction model of the track geometry detection system is established, and the error analysis and uncertainty evaluation of the track geometry detection system are carried out. The results show that the track geometry detection system calibrated by the dynamic calibration method proposed in this paper meets the requirements of the measurement error for the gauge and cross level. This study can establish the value traceability relationship of the track geometry detection system, realize the calibration and evaluation of the accuracy of the track geometry detection system under the real operation state, and improve the reliability and accuracy of the track geometry dynamic detection results.