Cratons are old and strong continental cores where the lithosphere is thick and remains largely undeformed for 2–3 b.y. Unlike typical cratons, the Wyoming craton underwent pervasive deformation ca. 80–55 Ma during the Laramide orogeny in the west-central United States, and has been subsequently encroached upon by the Yellowstone hotspot since 2.0 Ma. However, the mechanism for the deformation and the craton-hotspot interaction are not well understood. We present here a three-dimensional shear wave velocity model beneath the Wyoming craton constrained from Rayleigh wave data, which reveal new details about the cratonic lithosphere. The average lithosphere thickness beneath the craton is ∼150 km, significantly thinner than a normal cratonic root (>200 km). Continuous low velocities are observed beneath the Yellowstone hotspot and the Cheyenne belt. A low-velocity column is also present in the central-eastern craton at depths of 115–250 km. These low velocities can be explained by hot temperature and partial melting, implying mantle upwelling. A high-velocity anomaly with a dripping shape in central Wyoming extends to 200–250 km depth, indicating mantle downwelling and lithosphere erosion. Our model provides the first seismic evidence for complex small-scale mantle convection beneath the Wyoming craton. The convection probably developed during the subduction of the Farallon plate and has been reinforced by the Yellowstone hotspot. We propose that the combination of flat-slab subduction, small-scale convection, and hotspot activity can lead to massive destruction of a cratonic lithosphere.