;Crustal structure in eastern Taiwan is key for understanding the tectonic evolution and interaction between the Philippine Sea and Eurasian plates from subduction to collision. In order to explore the crustal structure in this region in detail, ambient noise tomography was used with a dense seismic array data set. We deployed 40 temporary seismic stations in Southeastern Taiwan in 2019 for about one month. Time series were cross-correlated to construct Rayleigh wave Green’s functions. For each station pair, group velocity dispersion curves were picked using a frequency-time analysis and image transformation technique. Then, we obtain surface-wave dispersions at 1–10 sec. Based on analyzing the maps of the ray paths, the results are highly correlated with surface geology for high frequency (1-5 sec) group velocities. The relatively high group velocities are mostly distributed in the Central Range, which is composed of metamorphic rocks. The relatively low group velocities are distributed in the Longitudinal Valley which is composed of sediments. In the Coastal Range mainly composed of sediments and andesite, the ray paths are with a range of velocities, which corresponding to the relatively varying rock distribution comparing with other regions. This study provides a fundamental data set of high-frequency dispersion curves (1-10s) in Southeastern Taiwan for establishing a fine velocity shallow structure in the whole of eastern Taiwan in the future.