Research on the infection risk of Flower yellowing disease (FYD) is crucial for promoting the sustainable cultivation of Zanthoxylum armatum DC. This study aimed to assess the potential distribution of FYD under current (1970–2000) and future (2041–2060 and 2061–2080) climate conditions across four Shared Socioeconomic Pathway scenarios (SSP126, SSP245, SSP370, and SSP585). A total of 80 occurrence records of FYD associated with Z. armatum were collected from Southwest China, together with 19 bioclimatic variables, one elevation variable, and eight edaphic variables. The MaxEnt model, optimized using the ENMeval package, was applied to predict the potential distribution of FYD. The results showed that all optimized models achieved a ΔAICc value of 0 and AUC values exceeding 0.90, indicating excellent predictive performance. Precipitation of the driest month (Bio_14), annual temperature range (Bio_7), precipitation seasonality (Bio_15), and elevation were identified as the dominant environmental factors influencing the potential distribution of FYD. Compared with the current period, future climate change is projected to markedly expand the area of high-suitability habitats for FYD, with major expansion concentrated in eastern Yunnan, southern Guizhou, and northern Sichuan. These findings suggest that enhanced field surveys, long-term monitoring, and targeted prevention strategies should be prioritized in projected expansion areas to reduce the potential risks of FYD to Z. armatum cultivation.