The agriculture sector is both a significant consumer of energy and water and a major source of environmental pollution and greenhouse gases. Soybean production (Glycine max) has experienced a fast growth and it is the fourth most widely cultivated crop, leading to serious environmental concerns. This study evaluates the energy, carbon, and water footprints of China’s soybean production so that key environmental impacts can be identified. To provide reliable results for decision-making, uncertainty analysis is conducted based on the Monte Carlo model. Results show that the impact on climate change, fossils depletion, ecosystem quality, human health, and resource was 3.33×103 kg CO2 eq (GSD2 = 1.87), 343.37 kg oil eq (GSD2 = 1.60), 6.18×10− 5 Species·yr (GSD2 = 1.81), 3.26×10− 3 DALY (GSD2 = 1.81), and 89.22 $ (GSD2 = 2.28), respectively. Freshwater ecotoxicity was the dominant contributor (77.69%) to the ecosystem quality category, while climate change (85.22%) was the dominant contributor to the human health category. Key factors analysis results show that diammonium phosphate and diesel, and on-site emissions from soybean production, were the major contributors to the overall environmental burden of soybean production. Several policy recommendations are proposed, focusing on trade structure optimization, technological improvements, and efficient resource use. Such policy recommendations provide valuable insights to those decision-makers so that they can prepare appropriate mitigation policies.