Understanding spatially and temporally explicit life cycle environmental impacts is critical for designing sustainable supply chains for biofuel and animal sectors. However, annual life cycle environmental impacts of crop production at county scale across mutiple years are lacking. To address this knowledge gap, this study used a combination of Environmental Policy Integrated Climate and process-based life cycle assessment models to quantify life cycle global warming (GWP), eutrophication (EU) and acidification (AD) impacts of soybean production in nearly 1000 Midwest counties yr^–1 over 9 years. Sequentially, a machine learning approach was applied to identify the top influential factors among soil, climate, and farming practices, which drive the spatial and temporal heterogeneity of life cycle environmental impacts. The results indicated that significant variations existed in life cycle GWP, EU, and AD among counties and across years. Life cycle GWP impacts ranged from −11.4 to 22.0 kg CO₂-eq kg soybean^–1, whereas life cycle EU and AD impacts varied by factors of 302 and 44, respectively. Nitrogen application rates, temperature in March and soil texture were the top influencing factors for life cycle GWP impacts. In contrast, soil organic content and nitrogen application rate were the top influencing factors for life cycle EU and AD impacts.