The invention discloses a shaft sealing water injection system of a main pump of a nuclear power station. The shaft sealing water injection system comprises an injection pump, a high-pressure cooler, a hydrocyclone, valves and a main connecting pipeline that are arranged at the exterior of the main pump, as well as an auxiliary pump and an internal runner that arranged in the main pump; the internal runner of the main pump is connected with an external runner of the main pump through a shaft sealing water injection hole and a high temperature water drainage hole that are formed in a main flange; and the injection pump, the high-pressure cooler and the hydrocyclone are sequentially arranged on the main connecting pipeline. The shaft sealing water injection system further comprises a bypass pipeline connected with the injection pump, the high-pressure cooler and the hydrocyclone in parallel; the main connecting pipeline is provided with a normally open main pipeline isolating valve at each of the two ends of a parallel connection section connected with the bypass pipeline in parallel; and the bypass pipeline allows low temperature upward filling water of a RCV system to be able to bypass the injection pump, the high-pressure cooler and the hydrocyclone and to directly enter the shaft sealing water injection hole of the main flange. Compared with the prior art, through redundancy design, and optimization of a system structure and control, the safety and the reliability of system operation and the maintainability of the shaft sealing water injection system are ensured.