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Abstract The Hawaiian‐Emperor seamount chain in the Pacific Ocean has provided fundamental insights into hotspot generated intraplate volcanism and the long‐term strength of oceanic lithosphere. However, only a few seismic experiments to determine crustal and upper mantle structure have been carried out on the Hawaiian Ridge, and no deep imaging has ever been carried out along the Emperor seamounts. Here, we present the results of an active source seismic experiment using 29 Ocean‐Bottom Seismometers (OBS) carried out along a strike profile of the seamounts in the region of Jimmu and Suiko guyots. Joint reflection and refraction tomographic inversion of the OBS data show the upper crust is highly heterogeneous withPwave velocities <4–5 km s⁻¹, which are attributed to extrusive lavas and clastics. In contrast, the lower crust is remarkably homogeneous with velocities of 6.5–7.2 km s⁻¹, which we attribute to oceanic crust and mafic intrusions. Moho is identified by a strongPmParrival at offsets of 20–80 km, yielding depths of 13–16 km. The underlying mantle is generally homogeneous with velocities in the range 7.9–8.0 km s⁻¹. The crust and mantle velocity structure has been verified by gravity modeling. While top of oceanic crust prior to volcano loading is not recognized as a seismic or gravity discontinuity, flexural modeling reveals a ∼5.0–5.5 km thick preexisting oceanic crust that is overlain by a ∼8 km thick volcanic edifice. Unlike at the Hawaiian Ridge, we find no evidence of magmatic underplating.