The effect of moisture content, temperature and fungal growth on quality of soybean was researched. The soybeans with moisture content of 11.2%, 11.8%, 12.7%, 13.9% and 14.7% were stored at 10, 15, 20, 25, 30, 35 ℃ respectively for 180 days. Fungal growth, the changes of germination rate and fatty acid value were determined. The results showed that during storage fungal growth was affected by the moisture contents and temperature, and the moisture content was the main factor to determine whether fungal growth or not, while the temperature affects the speed of the fungal growth. When soybeans were stored with the moisture content below 11.8%, which was the critical moisture content of fungal growth, the seed germination rate and fatty acid value was mainly affected by temperature; when soybeans were stored below 20 ℃, the seeds maintain relatively high germination rate; when stored above 30 ℃, the increase of the fatty acid value was intensified; when stored above the critical moisture content, seed germination rate and fatty acid value were affected by the synergy between fungal growth and temperature. High moisture content and fast fungal growth will lead to the deterioration of soybean quality in a certain extent, even stored in low temperature.