Extrusion tectonics driven by the collision of Indian-Eurasian continents and the relative motion among microcontinents (e.g. South China, Simao-Indochina blocks) has led to multi-phase and complex geological activity and structures in Northern Vietnam. While extensively studied, its detailed crustal architecture in association with multiple large-scale shear zones and plate boundaries remains unclear and is key to resolving long-lasting tectonic debates. This study constructs the first 3-D regional S-wave velocity (Vs) model with consistent P-wave velocity (Vp) and Vp/Vs ratio models by jointly using the crustal and head waves (e.g. Pg/Sg and Pn/Sn phases) from an augmented earthquake catalog combining the Vietnam National Earthquake Catalog (VNCAT) and the data from multiple adjacent seismic networks. The quality of phase picking and earthquake location incorporating seismic data from various sources are carefully examined and collected for the tomographic inversion. We use a stepwise joint inversion scheme to subsequently constrain the earthquake location, 1-D and 3-D velocity models. The output models suggest that the Song Ma suture represents a better candidate for the Indochina-South China boundary rather than the Red River Shear Zone. The latter seems to act as a crustal structure while the former and the Dien Bien Phu Fault are likely lithospheric ones. Several other geologic features such as the Tu Le volcanic basin, the Song Hong basin, and the Day Nui Con Voi metamorphic complex are also clearly depicted and discussed in the model. This new set of the Vp, Vs, and Vp/Vs models could further contribute to better assessment to seismic hazards in the northern Vietnam.