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The effects of long-term monocropping systems combined with climate on soil water aggregate stability (WSA) and soil fertility in the karst region of Southwest China (KRSWC) are unclear. Our research was conducted in the KRSWC, wherein tobacco (Nicotiana tabacum) production is characterized by heavy fertilization and continuous monocropping. The tobacco fields in the study area have similar soil types and fertilization and tillage practices and are spread over an area of 11,500 km2. A total of 568 topsoil samples were collected in 2021. Soil fertility was reflected using the soil fertility index (SFI), which was calculated using the minimum data set method with six soil fertility-related factors, namely, soil pH, soil organic matter, cation exchange capacity, available nitrogen, available phosphorus, and available potassium. Results showed that long-term planting generally promoted soil fertility levels and WSA content. WSA and SFI had inconsistent spatial distribution patterns likely due to different climate-driven effects. WSA variability was greatly controlled by precipitation (Spearman correlation coefficient [r] = −0.49, p < 0.01), whereas SFI variability was mostly dominated by temperature (r = −0.36, p < 0.01). The levels of SFI and WSA were optimal under conditions of low temperature and precipitation and poor under conditions of high temperature and precipitation. Moreover, long-term planting could alleviate the negative effects of climate on SFI and WSA in the KRSWC. The results of this study could provide valuable information on fertilization and climate-adapted strategies for tobacco fields in the KRSWC. [ABSTRACT FROM AUTHOR]