Through meticulous specimen classification and collation, a total of 41,912 flies, belonging to 42 families, was collected. The alpha-diversity analysis revealed significant differences (p < 0.05) across diverse regions and habitats. Specifically, fly diversity in the semi-humid zone was higher than that in the semi-arid zone. Moreover, the taiga-hardwood mixed forest and plantation forest exhibited relatively high levels of alpha-diversity. In the context of beta-diversity, the heterogeneity among different regions was at a medium level, jointly determined by beta sim and beta sne, with beta sim playing a dominant role. Conversely, the beta-diversity among different habitats shows a relatively high degree of similarity, with no distinct heterogeneity. Results from the redundancy analysis (RDA) and generalized additive model (GAM) indicated that climate and soil factors had a high explanatory power for fly diversity. Potential evapotranspiration, soil total nitrogen, and total potassium emerged as critical factors influencing fly diversity, soil porosity was the decisive factor, while the normalized difference vegetation index (NDVI) demonstrated varying effects in different models. Overall, fly diversity in the forests of eastern Inner Mongolia was at a relatively high level. Multiple environmental factors had thresholds in their impacts on flies, and these impacts varied across different environments. (c) 2025 National Science Museum of Korea (NSMK) and Korea National Arboretum (KNA). Publishing services by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).