Abstract: To analyze the impact mechanism of combination application of organic and inorganic fertilizer on the sustainable development of regional agricultural production system and to explore effective strategies for scientifically balancing regional planting and breeding industries, this paper used the emergy analysis method to evaluate the agricultural production system of Xinjiang Production and Construction Corps from 2000 to 2020. Additionally, scenario analysis was conducted to investigate the trends in sustainability indicators and their influencing factors. The results showed that the energy input of the agricultural production system of the Xinjiang Production and Construction Corps increased from 6.3×10²¹ sej in 2000 to 1.1×10²² sej in 2020, representing a 78.3% increase. Non-renewable industrial auxiliary energy 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 significantly from 4.5×10¹¹ sej∙¥⁻¹ in 2000 to 8.2×10¹⁰ sej∙¥⁻¹ in 2020, reflecting an 81.8% decline and indicating substantial improvements in economic efficiency. The environmental load rate 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), optimizing the fertilization structure alone, optimizing the fertilization structure and the amount increased the sustainability index by 5.2%−28.9% and 45.2%−62.2%, respectively. Methodologically, the combination application of organic and inorganic fertilizer reduced the input of non-renewable industrial auxiliary energy, increased the input of renewable organic energy, and reduced reliance on industrial production, thereby improving overall sustainability. It was recommended that the divisions and cities of the Xinjiang Production and Construction Corps set the organic fertilizer application rate for cotton and grain crops to 30%−50% (based on nitrogen calculation) and established long-term monitoring plots to assess fertilizer utilization efficiency; increased the purchase subsidies for manure return machinery to facilitate the final implementation of nutrient recycling.