Determining how the crustal structure developed in previous tectonic regimes influences current deformation is important for understanding seismogenic behavior. Paleozoic‐Mesozoic convergent‐margin tectonics produced the southeastern South Island crust, which is currently involved in late Cenozoic transpressional collision. We examine crustal velocity structure through joint inversion of earthquake travel times and ambient noise derived group velocities to increase the resolution of Vp (P‐wave velocity) and Vp/Vs across the region. This method improves the details of the shallow velocity structure and highlights lithological properties, uplifted regions, and distributed fracture zones. The Otago schist shows thick lower crust while contrasting higher Vp below 15 km depth characterizes the Matai terrane and Median batholith, both backstops during accretion and deformation. The complex velocity structure, integrated with late Cenozoic faults, structural domains, seismicity patterns, and geodynamic modeling, shows how Cenozoic structures relate to deeper properties. Seismicity within the schist is distributed within transition regions rather than along specific faults, and these zones contain low Vp and low Qp (1/attenuation). The most prominent seismicity zone is along the transition from northern Otago ranges to the Southern Alps, where faulting and brittle deformation corresponds to the eastern edge of ductile crustal thickening above the bending of the strong oceanic lower crust. The thick weak crust rheology of Otago, relative to Canterbury, enables broad deformation, with numerous late Cenozoic faults that may not persist to great depth. Along the southern stronger plutonic terranes, there is a band of sparse deeper (15–35 km) seismicity, consistent with strong elastic brittle crust.