A DTM map of the study area in the Taiwan Shoal was drawn based on precise and high-density data acquired in a field survey by a multi-beam sounding system (R2Sonic2024). We identified sand waves in the study area at water depths of 13.89–49.12 m; the main sand waves had heights of 5–25 m, lengths of 0.1–2.0 km, and crest lines 0.1–6.5 km long. The spatial distribution of the sand waves on the seabed is dense in the north and sparse in the south and the directions range between 50°–80° and 90°–135°. Between the main sand waves, secondary sand waves develop with heights of 0.1–5.0 m and lengths of 10–100 m, which are difficult to detect by satellite remote sensing. By comparing the evolution structures of the secondary and main sand waves, we identified three evolution modes of the secondary sand waves: parallel, oblique, and divergent modes according to the relative crest directions. Suitable water depth, reciprocating current speeds between 40 and 100 cm/s, and abundant sediment supply create favorable conditions for the formation of linear sand waves. Comparing the DTM maps and profiles of the June 2012 and June 2013 surveys of the same area, we found that the shape and morphology of the sand waves remained mostly unchanged under normal hydrodynamic conditions.