We refined the three-dimensional (3-D) Vp, Vs and Vp/Vs models around the San Andreas Fault Observatory at Depth (SAFOD) site using a new double-difference (DD) seismic tomography code (tomoDDPS) that simultaneously solves for earthquake locations and all three velocity models using both absolute and differential P, S, and S-P times. This new method is able to provide a more robust Vp/Vs model than that from the original DD tomography code (tomoDD), obtained simply by dividing Vp by Vs. For the new inversion, waveform cross-correlation times for earthquakes from 2001 to 2002 were also used, in addition to arrival times from earthquakes and explosions in the region. The Vp values extracted from the model along the SAFOD trajectory match well with the borehole log data, providing in situ confirmation of our results. Similar to previous tomographic studies, the 3-D structure around Parkfield is dominated by the velocity contrast across the San Andreas Fault (SAF). In both the Vp and Vs models, there is a clear low-velocity zone as deep as 7 km along the SAF trace, compatible with the findings from fault zone guided waves. There is a high Vp/Vs anomaly zone on the southwest side of the SAF trace that is about 1–2 km wide and extends as deep as 4 km, which is interpreted to be due to fluids and fractures in the package of sedimentary rocks abutting the Salinian basement rock to the southwest. The relocated earthquakes align beneath the northeast edge of this high Vp/Vs zone. We carried out a 2-D correlation analysis for an existing resistivity model and the corresponding profiles through our model, yielding a classification that distinguishes several major lithologies.