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The biodiversity hypothesis links urban species richness to human immunity, yet overlooks habitat heterogeneity that can quarantine pathogenic microbiota. We propose the β-diversity hypothesis: increased tree heterogeneity promotes urban microbial heterogeneity and improve human health. Using plant surveys and paired data of soil, phyllosphere and airborne microbiota transferred indoors (AMTI) across 72 Shanghai neighborhoods, we showed that elevated tree heterogeneity corresponds to higher β-diversity in both AMTI and soil communities. The spatial patterning of respiratory diseases (RDs) was driven by AMTI β-heterogeneity, revealing that homogenization of airborne microbiota affects human respiratory health. We further developed the urban tree βdis model and identified a threshold value of 0.661. Selecting phylogenetically distant tree families, e.g. Arecaceae, Oleaceae and Magnoliaceae at or above this threshold yields ready-to-use planting templates that maintains AMTI β-diversity and a scalable protocol for city-wide greening. Given microbial heterogeneity’s emerging health links, our findings call for embedding the β-diversity hypothesis into biodiversity–health frameworks and for cross-biome validation.