According to the requirements on manipulator robot in the electromagnetic compatibility measurement, this paper proposes the design methodology and control strategy of 6-DOF manipulator in emission source microscopy (ESM) task. The task constraints, the structure of the manipulator, orientation of the antenna and the integrity of scanning surface are modeled, and the ESM sampling cylinder is generated according to the principle of area optimization. The improved RRT∗ algorithm based on joint search strategy (RRT∗-JSS) realizes the optimal planning of the joint position state of the manipulator under a given scanning plane. In the simulation experiments, above method and strategy enable the manipulator to achieve a reduction of 68. 96% in the average joint change angle, under the scanning path loss of 4. 3%. In the verification experiment based on Elfin5 manipulator and patch-shaped radiation source, the error between the actual obtained ESM imaging and the simulation results is below 0. 35 dBm. Above simulation and experimental results prove the effectiveness of the studies, which is expected to apply in the field of EMI measurement.