The Huangshui River, a vital tributary in the upper reaches of the Yellow River within the eastern Qinghai–Tibet Plateau, is home to the endemic black fly species S. qinghaiense. In this study, we conducted a systematic survey of the distribution of the species in the Huangshui River basin, revealing its predominant presence along the river’s main stem. Based on four ecological niche models—MaxEnt with parameter optimization; GARP; BIOCLIM; and DOMAIN—we conduct a comparative analysis; evaluating the accuracy of AUC and Kappa values. Our findings indicate that optimizing parameters significantly improves the MaxEnt model’s predictive accuracy by reducing complexity and overfitting. Furthermore, all four models exhibit higher accuracy compared to a random model, with MaxEnt demonstrating the highest AUC and Kappa values (0.9756 and 0.8118, respectively), showcasing significant superiority over the other models (p < 0.05). Evaluation of predictions from the four models elucidates that potential areas of S. qinghaiense in the Huangshui River basin are primarily concentrated in the central and southern areas, with precipitation exerting a predominant influence. Building upon these results, we utilized the MaxEnt model to forecast changes in suitable areas and distribution centers during the Last Interglacial (LIG), Mid-Holocene (MH), and future periods under three climate scenarios. The results indicate significantly smaller suitable areas during LIG and MH compared to the present, with the center of distribution shifting southeastward from the Qilian Mountains to the central part of the basin. In the future, suitable areas under different climate scenarios are expected to contract, with the center of distribution shifting southeastward. These findings provide important theoretical references for monitoring, early warning, and control measures for S. qinghaiense in the region, contributing to ecological health assessment.