How to reduce the damage of conventional sterilization to the quality of prepared food, the primary indicator of consumer concern, remains an important challenge for food processing practitioners. The ZnO nanoparticles combined radio frequency (ZNCRF) has been developed previously by our research group. In this study, we explored the mechanism that the quality of chicken thigh meat samples of ZNCRF pasteurization was superior to that of conventional high pressure steam (HPS) sterilization from the perspective of the changes of protein and water state. The results showed that after processing by ZNCRF and HPS, the secondary structure of drumstick protein changed significantly, which the relative content of β-sheet in the samples decreased by 22.20% and 22.09%, respectively. The results of LF-NMR show that ZNCRF pasteurization (within 20 min) was helpful to improve the water retention and quality of chicken thigh meat products. The SEM showed that adopting ZNCRF processing (within 20 min) can be very good to retain the chicken thigh meat tissue microstructure. These differences were manifested in the sensory sense that the loss of color, texture, and flavor of the ZNCRF pasteurized chicken thigh meat samples was less than that of the HPS pasteurized samples. The results of this study provide a theoretical basis for the application of ZNCRF pasteurization in the chicken industry and the research of relevant sterilization equipment.