During the trough period after the grid-connected power generation of an Hydropower Station, due to the high bus voltage, the generator is in under - excitation operation for a long time, and the guide vane opening of the water turbine unit is small, and operation in the vibration zone will cause some damage to the water turbine unit, which can be solved by installing a high-voltage parallel reactor. The expansion under the full shutdown mode will seriously affect the economic benefits of hydropower stations and the grid structure. Therefore, this research studies the secondary system test scheme for the expansion project of 500kV hydropower station under the partial shutdown mode, and analysis in detail the changes of the protection configuration in the past during the expansion process. According to the analysis results, debugging methods such as the circuit wiring that needs to be removed after the protection configuration changes and the arrangement of secondary safety measures in this mode are put forward to eliminate potential safety hazards during the test. Through the expansion project of an Hydropower Station, the scheme demonstrates a highly secure and reliable solution that could also be referred to the future expansion of the hydropower station.