The Mexican subduction zone is a complex convergent margin characterized by a slab with an unusual morphology, an abnormal location of the volcanic arc, and the existence of slow earthquakes (slow slip events and tectonic tremors). The number of seismic imaging studies of the Mexican subduction zone has increased over the past decade. These studies have revealed the seismic wave velocity structure beneath Central and Southern Mexico. However, the existing tomographic models are either confined to specific areas or have coarse resolution. As a consequence, they do not capture the lateral and finer-scale variations in the mantle and the crust structure. Here, we fit frequency-dependent traveltime differences between observed and synthetic seismograms in a three-dimensional model of Central and Southern Mexico to constrain crustal and upper mantle seismic velocity structures jointly. We use ∼3,300 seismic records, filtered between 5 and 50 s, from 74 regional earthquakes. We perform point spread function tests to assess the resolution and trade-offs between model parameters. Our tomographic model reveals several seismic wave velocity features. These features include the geometry of the Cocos slab, the partial melting zone beneath the Trans-Mexican Volcanic Belt, and the Yucatan slab diving below Los Tuxtlas Volcanic Field that are consistent with previous studies. We also identify horizontal structures in the lower crust and the shallow upper mantle that were not previously identified. These structures include slow seismic wave velocity anomalies that may be correlated with ultra-slow seismic velocity zones and high conductivity regions, where slow earthquakes have been identified.