The crustal structure and Quaternary fault zone in the Seoul metropolitan area are investigated using a joint inversion that combines the receiver functions with surface wave dispersion based on seismic data from densely deployed seismic arrays. The uncertainty in inverted models is examined through a set of synthetic experiments. Synthetic tests and comparisons with other methods verify the observed crustal features. The Moho depths range between 28.7 and 32.8 km with relatively shallow depths in the central Seoul metropolitan area. The ratio varies between 1.67 and 1.85. A Conrad discontinuity with a weak velocity increase is present at a depth of ∼20 km. Low‐velocity anomalies appear at depths of ∼3 km and 6–11 km along the Chugaryeong fault zone and fault junction area. Apparent shear wave velocity contrasts appear across the fault zone where earthquakes are clustered. A high‐velocity block in the western Seoul metropolitan area lies along the fault zone that runs across western Seoul. The shear wave velocity models and seismicity suggest that the fault zone may extend to a depth of 11 km at least.