Improving seismic hazard mitigation of the densely populated metropolitan area of and around the capital of Taiwan requires detailed knowledge of the 3D crustal structure of Taipei basin. The high levels of ambient noise and the low levels of regional seismicity of this region complicate investigations of crustal structure with traditional seismic exploration or earthquake tomography methods. We investigate the shallow crust in the metropolitan region using surface wave array tomography with time domain empirical Green’s function (TDEGF) inferred from correlation of ambient seismic noise. Analysis of the TDEGF amplitudes suggests that the dominant sources of ambient seismic noise are the coastlines and shallow continental shelf of the Taiwan Strait, northwest of the study region. Our study demonstrates that ambient seismic noise tomography is feasible at periods of 0.5–3 s, which is much shorter than the 10–30 s used in most other studies, and which opens new opportunities for high resolution studies of near-surface heterogeneity. The lateral variation in Rayleigh wave phase velocity correlates well with surface geology and suggests that faults play an important role in the regional tectonic setting. High phase velocities mark the Tatun volcanic area, the Kuanyin Mountain dominated by Quaternary igneous rock, and the Miocene Western Foothills south of the Taipei fault. Low phase velocities characterize regions are along western and southeastern edges of the Taipei basin and the Pleistocene Linkou tableland. Main faults in the region are either marked by low phase velocities or define transitions between regions of high- and low-velocity anomalies.