To enhance the synchronization performance of multiple clocks in robotic communication systems, a study was conducted on a distributed clock synchronization compensation scheme. Quantitative compensation and dynamic compensation algorithms for clock errors were designed. The synchronization compensation scheme, based on the IgH EtherCAT communication protocol stack, was implemented, and trajectory tracking and communication performance tests were conducted on a six-axis robotic arm. The results show that the application of this synchronization scheme improves the circular trajectory precision of the robotic arm's end effector compared to non-IgH synchronization schemes. The clock synchronization error is reduced to 54 ns, with the error tolerance within ± 200 ns. It is evident that the compensation scheme enhances clock synchronization performance and meets the application requirements of the robotic arm.