Poor penetration was detected by ultrasonic testing on nuclear control rod guide tube assembly welded by electron beam welding. The welding contrast test on different batches of raw materials and other possible factors affecting the weld penetration were researched and analyzed. In order to reduce the effect of holes formed by non-metallic oxides and spiking defect in the raw material on weld penetration,the electron beam remelting process was used to prolong the high temperature residence time of weld deposit metal,and improve electron beam flow to conduct welding repair and process improvement. This method was verified by the process tests and can effectively solve the problem of weld penetration,and was successfully promoted and applied in follow-up projects.