Abstract In the context of rapid population growth and limited arable land resources, the agricultural system has to provide enough food in a sustainable way. Regional agricultural systems have good consistency in agricultural practices, management decisions, social economy, and climate, which is of great significance in ensuring food security. In this study, emergy analysis and the logarithmic mean divisia index method were integrated to construct an evaluation framework from the dimensions of socio-economic environment, resource environment, climate environment, and ecological environment. Then we evaluated and analyzed the changes in agricultural system sustainability from 1990 to 2019 in the mainstream of Liaohe River Basin, a typical agricultural basin in China. The results showed that the Emergy sustainability index (ESI) decreased from 0.17 to 0.14, and factors Δ Pt/Gt (social and economic development level), Δ G/I (agricultural economic benefits), and Δ Gt/G (economic structure) from the socio-economic environment dimension had the greatest impact on changes in ESI. Moreover, society and economy affected the factors in the resource environmental dimensions through the allocation of policies and resources, which in turn directly affected ESI. The influence of factors from the climatic environment and ecological environment weakens as the ability to manage agricultural systems increases. The research provided a reference for the planning and management of sustaining agricultural systems at a regional scale.