In this paper, an intrusion-tolerant synchronization control method based on the distributed intermediate observer is proposed for uncertain networked multi-axis motion control systems under network attacks. Firstly, the uncertainties are decomposed into matched and mismatched components. Then, the combined unknown input signals consisting of actuator attack, leader's non-zero input and matched uncertain components are estimated by the distributed intermediate observer. Based on the estimates, an intrusion tolerant synchronization control protocol is designed to compensate the matched unknown input effectively. At the same time, the mismatched uncertainties can be attenuated by adjusting the specific parameters. Finally, the satisfactory performance of intrusion tolerant synchronization control can be achieved.