We used transient electromagnetic (TEM) to map the hydrogeological structures in the Choushui River Alluvial Fan in Yunlin County of central Taiwan. A total of 63 TEM measurements were collected using the FASTSNAP system with 50 × 50 m in-loop configurations in the middle and distal fan. The 1D model, based on prior information, was constructed from the inverted soundings. Results showed a thin, resistive shallow layer and a 40 m low-resistive (6–42 ohm-m) zone beneath it. High-resistive zones (50–170 ohm-m) were found from 50–120 m depth, and low-resistive zones were revealed below 120 m in some areas. Results were consistent with resistivity and lithology logs from nearby wells. The inverted TEM models provide reliable subsurface information when prior informations of vertical electrical sounding and TEM were considered. We interpolated resistivity at 10 m, 50 m, 100 m, and 160 m depth from the 1D model results to produce a slice map of the area, which indicated variations, trends, and depths of the sediment deposits. The TEM method successfully identified the hydrogeological structures, showing that the upper 40 m of sediment acts as a confining layer for the aquifer structure from 50 m to 120 m depth.