With the increasing demand and limited production, China has to import a large amount of soybeans. However, soybean has been chosen as one target of the recent trade war between the US and China. It is therefore critical to assess the sustainability of soybean supply in China. Under such a circumstance, this study aims to fill such a research gap by using an emergy accounting approach from both spatial and temporal perspectives and at provincial-level. The impact of trade war on soybean imports and production is simulated by one GTAP (Global Trade Analysis Project) model. The results of Emergy Sustainability Indices (ESI) show that it is urgent to improve the sustainability of soybean planting in Heilongjiang, while Yunnan is the most appropriate place for planting soybean. For the international supply, the EER (Emergy Exchange Ratio) of China has decreased by 72% and the decrease of EERs at provincial level ranged from 59% to 86% during 2000–2015. The simulation results indicate the necessity of adjusting spatial structure of soybean planting and applying reasonable economic instruments to encourage sustainable soybean production.