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• Municipal tree canopy configuration is linked to adult mortality in Switzerland. • Higher canopy cover protects against cardiovascular mortality when configuration is fixed. • Aggregation and patch density show independent positive associations with mortality. • Balanced aggregation and fragmentation of tree canopies associate with lower mortality. • Findings guide urban greening strategies beyond canopy quantity toward spatial optimisation. The spatial distribution of tree canopies influences ecological functions and residents’ exposure to green spaces. Although several studies have examined green space configuration at neighborhood scales, evidence on tree canopy configuration at the municipal scale, an operational unit for urban planning, remains limited. We conducted a nationwide ecological study of 2,136 Swiss municipalities. Tree canopy coverage (PLAND), aggregation (AI, reflecting how tightly green patches are grouped together), patch density (PD, a measure of fragmentation), and area-weighted mean shape index (SHAPE_AM, a measure of shape complexity) were derived from 1-m canopy maps within municipality-specific populated areas. Natural-cause, cardiovascular, and cancer mortality (2017–2019) were obtained from the Swiss National Cohort. Fully adjusted negative binomial regression models estimated associations between canopy metric and mortality for each IQR increase in the metrics. Holding configuration constant, each IQR increase in canopy coverage (∼18%) was associated with a 3.6% [B: −0.036; 95% CI: −0.078 – 0.005] reduction in cardiovascular mortality. Higher aggregation corresponded to a 4.3% [B: 0.043; 95% CI: 0.026–0.061], an 8.9% [B: 0.089; 95% CI: 0.059–0.119], and a 2.1% [B: 0.021; 95% CI: 0–0.042] higher number of natural-cause, cardiovascular, and cancer deaths respectively. Higher fragmentation was associated with a 3.3% [B: 0.033; 95% CI: 0.016–0.050], a 4.9% [B: 0.049; 95% CI: 0.020–0.078], and a 2.2% [B: 0.022; 95% CI: 0.001–0.043] increase in these causes respectively. No meaningful associations were observed between shape complexity and any mortality outcomes. Associations for aggregation and fragmentation were generally stronger in highly urbanized municipalities. At the municipal scale, mortality was lower where tree canopy was distributed across several moderately sized, spatially balanced patches rather than highly aggregated or highly fragmented structures. These findings suggest that urban greening strategies should optimize its spatial configuration to maximize health benefits.