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Abstract Microclimate heterogeneity in Southeast Asia and its implications for biodiversity remain understudied. We investigated microclimate changes between 1982 and 2017 using high‐resolution data and a patch‐mosaic model. Our findings reveal a decline in microclimate heterogeneity (as indicated by Shannon's diversity index) and a significant increase in elevation. Topographical factors (∼50.6%) and climatic factors (∼21.5%) primarily influenced the decline. Spatial heterogeneity weakened with larger moving windows and coarser grid‐scale data sets. Our study suggests that shifting mountainous microclimates play a crucial role in mediating biodiversity in Southeast Asia.