In order to explore the characteristics of the periphytic algae community structure and its relationship with environmental factors in the Taiyuan region of the Fenhe River, a total of six sampling sites were investigated in July and December 2021. The effects of water quality status and environmental factors at each sampling point on the community structure of epiphytes were detected. The results showed that a total of 7 phyla and 54 genera of periphytic algae were identified in the Taiyuan region of the Fenhe River, and the species composition was mainly Bacillariophyta, Cyanophyta, and Chlorophyta. According to the analysis results of the biodiversity index, the water body of the Taiyuan region of the Fenhe River is in a state of moderate pollution. The correlation analysis between the epiphytic algae and environmental factors showed that the cell density of algae was significantly correlated with dissolved oxygen (DO), phosphate (PO3− 4-P), chemical oxygen demand (COD), total phosphorus (TP), and transparency (SD) in the wet season. The algal cell density in the dry season was significantly correlated with water temperature (WT), TP, PO3− 4-P, and COD. According to the redundancy analysis, the community distribution of the epiphytic algae in the Taiyuan region of the Fenhe River was closely related to physical and chemical factors such as COD, nitrate nitrogen (NO− 3-N), WT, dissolved organic carbon (DOC), total nitrogen (TN), and TP, and COD is the main environmental factor driving the change in the community distribution of the periphytic algae in the wet season. TN is the main control factor driving the change in the biological community distribution of periphytic algae in the dry season.