Abstract: This study used emergy analysis to evaluate the agricultural production system of the Xinjiang Production and Construction Corps (XPCC) from 2000 to 2020; it analyzed the mechanisms by which the combined application of organic and inorganic fertilizers affects the sustainable development of regional agricultural production systems, and explored effective strategies for scientifically balancing regional planting and breeding industries. Additionally, scenario analysis was conducted to investigate influencing factors and trends in sustainability indicators. The results showed that emergy inputs to the agricultural production system of XPCC increased from 6.3×10²¹ sej in 2000 to 1.1×10²² sej in 2020, representing a 78.3% increase. Non-renewable industrial auxiliary emergy and renewable environmental resources were the primary sources, contributing 33.1%−49.2% and 32.7%−39.7%, respectively. The emergy input per unit output value decreased from 4.5×10¹¹ sej∙¥⁻¹ in 2000 to 8.2×10¹⁰ sej∙¥⁻¹ in 2020, representing a 81.8% decline and indicating substantial improvements in economic efficiency. The environmental load ratio showed an overall upward trend, reaching 1.15 in 2020, an increase of 64.1% from 2000, suggesting growing environmental pressure. Meanwhile, the sustainability index exhibited a general downward trend, decreasing by 44.3% over the study period to reach 1.42 in 2020. Compared with the baseline scenario (BAU), the scenarios optimizing the fertilization structure alone and optimizing both fertilization structure and amount increased the sustainability index by 5.2%−28.9% and 45.2%−62.2%, respectively. Methodologically, the combined application of organic and inorganic fertilizers reduced the input of non-renewable industrial auxiliary emergy, increased the input of renewable organic emergy, and reduced reliance on industrial production, thereby improving overall sustainability. It is recommended that the divisions and cities of XPCC set the organic fertilizer application rate for cotton and grain crops to 30%−50% (based on nitrogen content); establish long-term monitoring plots to assess fertilizer utilization efficiency; and increase purchase subsidies for manure-return machinery to facilitate the implementation of nutrient recycling.