We investigate the geometry of the Moho interface in the southern California region including the San Andreas fault (SAF), San Jacinto fault zone (SJFZ), Elsinore fault (EF) and Eastern California Shear Zone with systematic analysis of receiver functions. The data set consists of 145 teleseismic events recorded at 188 broadband stations throughout the region. The analysis utilizes a 3D velocity model associated with detailed double-difference tomographic results for the seismogenic depth section around the SAF, SJFZ, and EF combined with a larger scale community model. A 3D ray tracing algorithm is used to produce effective 1D velocity models along each source-receiver teleseismic ray. Common Conversion Point (CCP) stacks are calculated using the set of velocity models extracted for each ray. The CCP stacks are analyzed with volumetric plots, maps of maximum CCP stack values, and projections along profiles that cross major faults and other features of interest. The results indicate that the Moho geometry in the study area is very complex and characterized by large prominent undulations along the NE–SW direction. A zone of relatively deep Moho (~35–40 km) with overall N–S direction crosses the SAF, SJFZ, and EF. A section of very shallow Moho (~10 km) below and to the SE of the Salton Trough, likely associated with a young oceanic crust, produces large Moho offsets at its margins. Locations with significant changes of Moho depth appear to be correlated with fault complexity in the brittle crust. The observations also show vertical Moho offsets of ~8 km across the SAF and SJFZ close to Cajon pass, and sections with no clear Moho phase underneath Cajon pass and adjacent to the SJFZ near Anza likely produced by complex local velocity structures in the brittle upper crust. These features are robust with respect to various parameters of the analysis procedure.