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Abstract The Formosa array, with 137 broadband seismometers and ∼5 km station spacing, was deployed recently in Northern Taiwan. Here by using eight months of continuous ambient noise records, we construct the first high‐resolution three‐dimensional (3‐D) shear wave velocity model of the crust in the area. We first calculate multi‐component cross‐correlations to extract robust Rayleigh wave signals. We then determine phase velocity maps between 3 and 10 s periods using Eikonal tomography and measure Rayleigh wave ellipticity at each station location between 2 and 13 s periods. For each location, we jointly invert the two types of Rayleigh wave measurements with a Bayesian‐based inversion method for a one‐dimensional shear wave velocity model. All piecewise continuous one‐dimensional models are then used to construct the final 3‐D model. Our 3‐D model reveals upper crustal structures that correlate well with surface geological features. Near the surface, the model delineates the low‐velocity Taipei and Ilan Basins from the adjacent fast‐velocity mountainous areas, with basin geometries consistent with the results of previous geophysical exploration and geological studies. At a greater depth, low velocity anomalies are observed associated with the Linkou Tableland, Tatun Volcano Group, and a possible dyke intrusion beneath the Southern Ilan Basin. The model also provides new geometrical constraints on the major active fault systems in the area, which are important to understand the basin formation, orogeny dynamics, and regional seismic hazard. The new 3‐D shear wave velocity model allows a comprehensive investigation of shallow geologic structures in the Northern Taiwan.