In order to understand the changes of quality indexes and provide new insights for the scientific storage and the predictionof quality change of high oil soybean during storage. In the present study, a biochemical investigation was carried out to determine the quality indicators of high-oil soybeans during seed storage. Two kinds of high-oil soybeans were collected from the Henan and Inner Mongolia of China. Different moisture (13.00%±0.20% and 15.00%±0.20%) were then adjusted and stored the seeds at 25℃ and 35℃ for 180 days. The quality indexes of high-oil soybeans were determined and analyzed every 30 days during storage. Some parameters were evaluated, including the malondialdehyde (MDA) content, electrical conductivity, and enzyme activities of catalase (CAT), as well as the peroxidase (POD) and polyphenol oxidase (PPO). A correlation analysis was also carried out between the physiological and biochemical indexes. A kinetic model was selected for the change trends analysis of electrical conductivity and MDA. The results showed that the activities of CAT, POD, and PPO decreased with the increase in storage time, whereas the electrical conductivity and MDA content increased significantly in the two kinds of high-oil soybeans. And the change range of them increased with the increasing of the initial moisture content and the storage temperature. The correlation analysis showed that the storage time presented a significant or extremely significant correlation with the physical and chemical indexes of the two high-oil soybeans. The correlation coefficients between the storage time with the MDA and PPO were 0.82 and -0.90, 0.81 and -0.92, in the Henan and Inner Mongolia soybeans, respectively. The initial water content was significantly negatively correlated with the CAT activity of the two soybeans. The correlation coefficients were -0.63 and -0.74, respectively, indicating no strong correlation with the indicators. At the same time, there was a positive correlation between the storage temperature and the electrical conductivity in the two soybeans, where the correlation coefficients were 0.66 and 0.61, respectively. Furthermore, the kinetic analysis showed that the zero-order kinetic model better fitted for both electrical conductivity and MDA of the two high-oil soybeans at different storage temperatures. The two indexes were attributed to the energy demand reaction during storage (ΔG>0). The zero-order kinetic response coefficient also increased with the increase of initial moisture content and storage temperature of soybeans. Moreover, there was a higher content of crude fat in the zero-order kinetic activation energy of MDA and the electrical conductivity in the Henan soybean, compared with the Inner Mongolia one. Consequently, the higher temperature, initial moisture content, and crude fat content accelerated the electrical conductivity and MDA during storage, leading to the faster quality deterioration of the high-oil soybean. Therefore, a strict control of the temperature and initial moisture content during storage can be expected to maintain the fat content of seeds for the less quality deterioration of high-oil soybean. In particular with the high initial moisture content, the temperature conditions should be strictly regulated for the storage safety of the soybeans. Meanwhile, MDA content of high-oil soybean was more likely to change during storage than other indexes, which could be used as an early reference index for the quality change prediction.