The accuracy of digital elevation models (DEMs) is crucial for properly estimating flood inundation area. DEM pixel size is especially important when generating flood inundation maps of small streams with a channel width of less than 50 m. In Korea, DEMs with large spatial resolutions of 30 m have been widely applied to generate flood inundation maps, even for small streams. Additionally, when making river master plans, field observations of stream cross-sections, as well as reference points in the middle of the river, have not previously been used to enhance the DEM. In this study, it was graphically demonstrated that high-resolution DEMs can increase the accuracy of flood inundation mapping, especially for small streams. Also, a methodology was proposed to modify the existing low-resolution DEMs by adding additional survey reference points, including river cross-sections, and interpolating them into a high spatial resolution DEM using the inverse distance weighting method. For verification purposes, the modified DEM was applied to Han stream on Jeju Island. The modified DEM showed much better accuracy when describing morphological features near the stream. Moreover, the flood inundation maps were formulated with the original 30 m pixel DEM and the modified 0.1 m pixel DEM using HEC-RAS modeling of the actual flood event of Typhoon Nari, and then compared with the flood history map of Nari. The results clearly indicated that the modified DEM generated a similar inundation area, but a very poor estimate of inundation area was derived from the original low-resolution DEM.