The gear is the core component of numerous mechanical transmission systems. Accurately and efficiently measuring the tooth flank deviation during the manufacturing process is crucial to improve its accuracy. However, the existing on-machine measurement methods are usually contacted which are limited in measurable information and efficiency, and easily inevitably cause surface scratches due to the contact between the probe and tooth flank. Therefore, an on-machine measurement method based on line laser scanning for gear deviation is proposed in this paper. Firstly, an on-machine measurement kinematics model of gear deviation based on machine tool topology and homogeneous transformation theory is established. Then, a gear deviation calculation method is proposed according to the characteristics of the three-dimensional point cloud. Finally, the measurement experiments are conducted, and the gear accuracy level is 8 which is consistent with the accuracy level obtained by the gear measurement center. Thus, it proves the measurement accuracy of the proposed method, which can offer guidance for closed-loop precision manufacturing of gear machining, measurement, compensation, and re-machining.