This research identified harmful fungi that cause soybean pod and seed decay in China’s Sichuan Province. Scientists found eight different Fusarium species and six different Colletotrichum species affecting soybean pods, with some species identified for the first time as soybean pathogens. Laboratory tests showed that certain fungal species, particularly Fusarium proliferatum and Colletotrichum fructicola, were the most damaging to soybean plants. These findings help farmers understand and better manage fungal diseases in soybean crops grown in intercropping systems.