Abstract The mechanisms underlying the patchy distribution of forearc megathrust earthquakes and arc volcanoes in subduction zones remain poorly understood. Here we present a high‐resolution seismic tomographic model of the Central American subduction zone, derived from a joint inversion of local body‐wave and teleseismic Rayleigh‐wave data. Our model reveals significant along‐trench structural heterogeneities in the crust and upper mantle, closely matching segmentation patterns in the forearc megathrust and arc volcanism. Large megathrust earthquakes (Mw ≥ 7.0) cluster where the Cocos slab is underlain by subslab low‐velocity anomalies, suggesting that localized accumulation of buoyant asthenosphere may contribute to the megathrust segmentation. Active arc volcanoes align with discrete low‐velocity anomalies in the crust and mantle wedge, indicating spatial variations in partial melting or magma source enrichment. Slab rollback beneath Nicaragua and toroidal mantle flow beneath Costa Rica may drive along‐arc geochemical variations. Collectively, the structural heterogeneities influence the segmentation of seismicity and volcanism in Central America.