Cold and excess moisture pose a serious threat to soybean production especially during seed germination in short-season environments. In this study, the effects of low temperature and excess moisture stress on seed germination were investigated in 187 soybean accessions originating from 18 countries. The experiment used a combination of three temperature conditions (i.e., 20 °C/14 °C, 14 °C/10 °C, and 10 °C/10 °C day/night) and two moisture levels (i.e., normal and excess). The seed germinability traits measured included germination rate (GR), germination index, germination time, germination uniformity, and coefficient of velocity of germination. Overall, GR was lowest in the 20 °C/14 °C + excess moisture and germination time was longest in the 10 °C/10 °C + excess moisture. When compared with 20 °C/14 °C + normal moisture treatment, GR at 10 °C/10 °C + excess moisture decreased by 38%; germination time increased by 20 days; seed viability decreased by 83%; germination uniformity decreased by 70%; germination speed decreased by 73%. Differences in GR, germination index, and germination velocity under different treatments were affected by temperature, moisture, and their interaction. Variation in germination time uniformity was determined by temperature, with no significant effects of moisture conditions and the interaction of temperature and moisture. It was shown that the temperature–excess moisture interaction led to a sharp decrease in seed germination. Two genotypes including PI 603147 and PI 507702 were identified with a GR over 90% at 10 °C/10 °C + excess moisture. This study generated new knowledge and data to further the understanding of genetic resistance to cold and excess moisture stress in soybean.