Our aim is to analyze the emergy evaluation indicators of the agricultural ecosystem in Dazhou, northeastern Sichuan, and provide practical and effective recommendations for sustainable agricultural development. Using emergy analysis, the emergy inputs and outputs of an agricultural ecosystem from 2002 to 2022 were calculated. Five emergy indicators were selected for evaluation: emergy yield ratio (EYR), emergy self-sufficiency ratio (ESR), emergy input ratio (EIR), environmental load ratio (ELR), and emergy sustainable indices (ESI). The total emergy input of the agricultural ecosystem showed an upward trend from 2002 to 2017, thus the industrial auxiliary emergy input decreased, somewhat curbing its continued rise from 2017 to 2022. The structure of emergy inputs, in descending order, is as follows: industrial auxiliary > organic emergy > renewable environmental resources > non-renewable environmental resources. The total emergy output of the agricultural ecosystem was highest in 2007, reaching 2.31 × 1022 Sej, and lowest in 2012, at 1.83 × 1022 Sej. The structure of emergy outputs, in descending order, is as follows: livestock > planting > fishery > forestry. The emergy yield ratio fluctuated down from 3.12 to 2.51, with an average of 2.88, below the provincial average of 3.07. The emergy self-sufficiency ratio fluctuated down from 0.30 to 0.26, with an average of 0.27, above the provincial average of 0.13. The emergy input ratio fluctuated up from 2.31 to 2.91, with an average of 2.66, above the provincial average of 1.86. The environmental load ratio fluctuated from 3.8 to 4.75, with an average of 4.40, which is higher than the provincial average of 1.68. The emergy sustainable indices fluctuated down from 0.81 to 0.53, with an average of 0.67, below the provincial average of 1.17. The efficiency of resource utilization in the agricultural ecosystem of Dazhou has decreased, economic inputs have increased, and it is in a consumptive production process. The pressure on the local natural environment is increasing, and the capacity for sustainable development remains at a low level over the long term.