Distribution of fish community depends largely on environmental disturbance such as habitat change. In this study, we evaluated the impact of environmental variables and microhabitat patch types on fish distribution in Yudeung Stream at 15 sites between early May and late June 2019. We used non-metric multidimensional scaling to examine the distribution patterns of fish in each site. Gnathopogon strigatus, Squalidus gracilis majimae, Zacco koreanus, and Zacco platypus were associated with riffle and boulder areas, whereas Iksookimia koreensis, Acheilognathus koreensis, Coreoleuciscus splendidus, Sarcocheilichthys nigripinnis morii, and Odontobutis interrupta were associated with large shallow areas. In contrast, Cyprinus carpio, Carassius auratus, Lepomis macrochirus, and Micropterus salmoides were found at downstream sites associated with large pool areas, sandy/clay-bottomed areas, and vegetated areas. On the basis of these results, we suggest that microhabitat patch types are important in determining the diversity and abundance of fish communities, since a mosaic of different microhabitats supports diverse fish species. As such, microhabitat patches are key components of freshwater stream ecosystem heterogeneity, and a suitable patch composition in stream construction or restoration schemes will support ecologically healthy food webs.