We introduce a real-time motion control system that uses the EtherCAT protocol and apply it to a manipulator with six degrees of freedom. The complexity of a multi-joint manipulator leads to higher requirements for synchronous and real-time performance. EtherCAT technology can greatly improve the performance in terms of accuracy, speed, capability, and band width in industrial control, which is crucial in our robot projects. In this paper, we discuss a servo motion control system based on EtherCAT using IgH as the open-source master station. A Linux operating system is adopted because of the advantages of open-source, high-efficiency, and high-stability operation as well as multi-platform support, which provide more flexibility, freedom, and extendability to developers. Considerable research has been conducted to explore EtherCAT technologies, completely implementing home-made codes with the aid of open-source libraries, debugging the master-slave communication process, and testing the resulting motion controller running on Linux or POSIX-compatible operating systems. To improve the real-time response of servo control, a real-time Xenomai kernel has been compiled, adopted, and tested, and it showed significant enhancement of the real time of a servo motion control system. Furthermore, we explore trajectory planning and inverse kinematic solutions. A trajectory planning method based on B-spline interpolation of three degrees, which makes each part of the trajectory planning curve have relative independence and continuity, is proposed for the kinematic trajectory planning problem in Cartesian space. A coordinate system is established using the modified D-H parameters method to obtain the inverse kinematics of the manipulator. The simulation and experimental results show that the calculation speed of inverse solutions is excellent and the motion of the manipulator is continuous and smooth.