The shaft seal of the pre-lubricated oil pump for the emergency diesel engine in a nuclear power plant is a skeleton oil seal. After about one year of operation, oil will leak from the shaft seal and enter the drive motor, affecting the operation reliability of the emergency diesel engine. By building a numerical simulation platform, the thermal-structure coupling analysis of the skeleton oil seal were carried out and the contact pressure, deformation, Von Misses stress contour and temperature contour of the skeleton oil seal under actual working conditions were studied. Through the establishment of a sealing test device, sealing tests for the concentric smooth shaft, the concentric shaft with a groove on the sealing contact surface, and the eccentricity shaft with a groove on the contact surface were carried out under different shaft surface roughness and hardness. And the influence on the sealing performance of the oil seal was analyzed. The morphology of the sealing lip and the change of material functional groups before and after the trial were analyzed. The study results show that the accuracy and surface quality of the shaft where the oil seal is installed will affect the sealing performance of the oil seal; the main reason for the failure of the skeleton oil seal of the pre-lubricating oil pump is the long-term wear of the transmission shaft and oil seal, which forms grooves on the shaft; and the formation of the grooves will lead to increased leakage. Therefore, improving the wear resistance of the drive shaft is a key. The research results have high reference value for the exploration of the sealing principle of the same type of skeleton oil seal and the analysis of the reasons for the failure of the seal.