Bisphenol A (BPA) reportedly exerts concentration-dependent effects on plant growth, based on hydroponic exposure experiments. However, this pattern might differ in soil substrate, and the effects of different BPA concentrations in soil on crop germination as well as symbiotic relationship with rhizobia remain largely unclear. In this study, we evaluated the effects of different BPA concentrations (0, 10, 20, 40, 80, 160, and 320 mg/kg air-dry soil) on soybean growth index, germination, and root nodule by soil culture experiments. Results showed that low-dose BPA (10 mg/kg) treatment resulted in a 38.0 and 59.4% increase in total biomass and yield, respectively, while germination time was shortened by 10.1%. Conversely, high-dose BPA treatment significantly inhibited total biomass, yield, and germination time by an average of 39.9, 35.4, and 31.3% in 160 and 320 mg/kg, respectively. Root nodule biomass decreased in all BPA treatments, especially significantly decreased evenly by 66.6% in high concentrations of 160 and 320 mg/kg. Furthermore, germination time significantly explained variations of total biomass and yield by 19.2 and 18.3%, whereas nodule biomass significantly explained by 40.4 and 26.2%, respectively. The structural equation modeling revealed that BPA inhibited soybean total biomass and yield by prolonging germination time and inhibiting soybean nodule formation, while nodule biomass exhibited a larger path coefficient (0.553 and 0.475) than germination time (− 0.252 and − 0.280), suggesting a more important role of soybean nodule. Collectively, these findings provide invaluable insights into the mechanisms underlying the effects of BPA on crop growth.