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To meet the sustainable development goals in rocky desertified regions like Guizhou Province in China, we should maximize the crop yield with minimal environmental costs. In this study, we first calculated the yield gap for 6 main crop species in Guizhou Province and evaluated the quantitative relationships between crop yield and influencing variables utilizing ensembled artificial neural networks. We also tested the influence of adjusting the quantity of local fertilization and irrigation on crop production in Guizhou Province. Results showed that the total yield of the selected crops had, on average, reached over 72.5% of the theoretical maximum yield. Increasing irrigation tended to be more consistently effective at increasing crop yield than additional fertilization. Conversely, appropriate reduction of fertilization may even benefit crop yield in some regions, simultaneously resulting in significantly higher fertilization efficiency with lower residuals in the environment. The total positive impact of continuous intensification of irrigation and fertilization on most crop species was limited. Therefore, local stakeholders are advised to consider other agricultural management measures to improve crop yield in this region. [ABSTRACT FROM AUTHOR]