Summary Mexico has a complex geological history that is typified by the distinctive terranes that are found in the south-central region. Crustal thickness variations often correlate with geological terranes that have been altered by several processes in the past, for example aerial or subduction erosion, underplating volcanic material or rifting but few geophysical studies have locally imaged the entire continental crust in Mexico. In this paper, the thickness of three layers of the crust in south-central Mexico is determined. To do this, we use P- and S-wave receiver functions (RF) from 159 seismological broad-band stations. Thanks to its adaptive nature, we use an empirical mode decomposition (EMD) algorithm to reconstruct the RFs into intrinsic mode functions (IMF) in order to enhance the pulses related to internal discontinuities within the crust. To inspect possible lateral variations, the RFs are grouped into quadrants of 90°, and their amplitudes are mapped into the thickness assuming a three-layer model. Using this approach, we identify a shallow sedimentary layer with a thickness in the range of 1–4 km. The upper-crust was estimated to be of a few kilometers (<10 km) thick near the Pacific coast, and thicker, approximately 15 km in central Oaxaca and under the Trans-Mexican Volcanic Belt (TMVB). Close to the Pacific coast, we infer a thin crust of approximately 16 ± 0.9 km, while in central Oaxaca and beneath the TMVB, we observe a thicker crust ranging between 30 and 50 km ± 2.0 km. We observe a crustal thinning, of approximately 6 km, from central Oaxaca (37 ± 1.9 km) towards the Gulf of Mexico, under the Veracruz Basin, where we estimate a crustal thickness of 31.6 ± 1.9 km. The boundary between the upper and lower crust in comparison with the surface of the Moho do not show significant variations other than the depth difference. We observe small crustal variations across the different terranes on the study area, with the thinnest crust located at the Pacific coast and Gulf of Mexico coast. The thickest crust is estimated to be in central Oaxaca and beneath the TMVB.