Soybean is the most important oilseed and feed crop globally. As one of the major soybean producers in the world, soybean yield variability in the United States has garnered widespread attention. We analyze the effect of the Indian Ocean sea surface temperature (SST) on soybean yield variability. Our findings indicate that variations in Indian Ocean SST during the November–December–January (hereinafter referred to as ND(-1)J) period, approximately nine months prior to harvest, account for 16 % of the anomaly in U.S. soybean yields. Furthermore, for each standard deviation change in the Indian Ocean Basin (IOB) index, there is an estimated 4.0 % change in total soybean production in the United States. The root zone soil moisture and maximum temperature during the reproductive growth stage in summer are the key factors influencing the United States soybean yields. The warming of the Indian Ocean could cause hot and dry conditions during July-August-September (JAS) by influencing ND(-1)J soil moisture and the eastern Pacific SST, leading to substantial soybean failures in the United States. Our findings emphasize the importance of the Indian Ocean SST on soybean production in the United States and reveal the pathways of this impact, which can help predict the United States soybean failures and improve food security worldwide.