Vibration and noise problems of the gear system have been widely concerned in recent years. A study of transmission error is conducted to verify the sources of the vibration and noise. The tooth meshing process is analyzed with consideration of the shaft, bearing, box, tooth deformation, and tooth micro-modification in this paper. The transmission error of a two-stage gearbox is discussed based on a theoretical calculation model of gear transmission error. Then the transmission error is measured in different conditions on a test system of two-stage gearbox. By comparing to the test data, the theoretical model of the two-stage transmission error has been refined and a more reasonable model is presented. The study plays an important role in reducing vibration and noise of the gear system.