Abstract: Soil-borne fungal plant pathogens pose significant threats to agricultural productivity, with their impact influenced by cropping systems. Mild salinity-alkalinity stress, increasingly prevalent in northern agricultural regions, can exacerbate the impact of pathogens on crops. However, the host-specificity of soil-borne fungal pathogens in various cropping systems remains largely unknown, particularly in mildly saline-alkaline soils, impeding the design for sustainable agricultural practices. Here, we hypothesized that reducing host density in crop rotations could mitigate the abundance of host-specific pathogens under mild salinity-alkalinity conditions. In a thirteen-year field experiment conducted in a mildly saline-alkaline environment, we examined soil-borne fungal pathogen communities and their host-specificity in three different cropping systems: maize monoculture (M), maize-wheat rotation (MW) and maize-wheat-soybean (MWS) rotation systems. Using amplicon sequencing and literature review, we determined the effects of host density and soil nutrient availability on pathogen abundance. We found that soil-borne fungal communities significantly affected by cropping systems under mild salinity-alkalinity stress. Host-specific pathogens were diluted by 68.9-90.0% in reducing host density. Specifically, maize-pathogen, i.e. Ustilago maydis, was lower in soils from MWS and MW than in M, mainly related to the reduced availability of soil nutrients. Wheat-pathogens, i.e. Bipolaris sp., decreased in soil from MWS than MW, but increased than M, correlating with reduced host density. In contrast, generalist-pathogens increased in soil from MW than M, associated with soil nutrient availability. Our work suggests the differential responses of host-specific and generalist soil-borne fungal pathogens to different long-term cropping systems. Host-specific pathogens could be reduced by reducing host density in our study. Furthermore, we highlight the potential effects of host density and soil nutrient availability in mitigating pathogen abundance. This study highlights distinct responses of host-specific and generalist soil-borne pathogens to cropping systems under mild salinity-alkalinity stress. Regulating host planting density and managing soil nutrient availability could support the development of more sustainable disease management strategies in saline-alkaline farmland.