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In subduction zones, along‐strike and downdip variations in megathrust slip behavior are linked to changes in the properties of the subducting and overriding plates. Although marine geophysical methods provide insights into subduction zone structures, most surveys consist of sparse 2D profiles, limiting our understanding of first‐order controls. Here, we use active‐source seismic data to derive a 3D crustal‐scale P‐wave velocity model of the Alaska Peninsula subduction zone that encompasses both plates and spans the Semidi segment and SW Kodiak asperity. Our results reveal modest variations within the incoming plate, attributed to a series of fracture zones, seamounts and their associated basement swell, collectively contributing to plate hydration. Basement swell appears to modulate the distribution and type of sediment entering the trench, likely impacting observed variations in slip behavior. The overriding plate exhibits significant heterogeneity. The updip limit and width of the dynamic backstop are similar between the SW Kodiak asperity and eastern Semidi segment but differ significantly from the Western Semidi segment. These distinctions likely account for differences in earthquake rupture patterns and interseismic coupling among these segments. Additionally, high velocities in the mid‐lower forearc crust coincide with the location of the megathrust slip during the Mw 8.2 2021 Chignik event. We interpret these velocities as intracrustal intrusions that contributed to the deep rupture of the 2021 event. Our findings suggest that the contrasting structural and material properties of both the incoming and overriding plates influence the spatially complex and semi‐persistent segmentation of the megathrust offshore the Alaska Peninsula.