Underground coal mining in the Huainan coal mine areas, Anhui, China, has created numerous small artificial lakes, which provide excessive water storage space as well as ecological benefits. Characterization of these freshwater ecosystems might have important implications on ecological rehabilitation and recovery in the mining areas. Phytoplankton community structure can provide important eco-environmental information in different habitats besides playing fundamental roles in trophic structures of the lake ecosystem. This study aimed to classify the phytoplankton community on the basis of functional groups (FGs), which has been reported to be more useful than the traditional taxonomic grouping methods for elucidating the ecological functions of phytoplankton. Three small lakes at the PXPJ, PXGQ, and PXXQ sites in Huainan Panxie coal mine areas were selected as representative research sites considering their ecological conditions, and the phytoplankton community structure and water quality at these sites were assessed from 2013 to 2014. Next, the seasonal succession of phytoplankton FGs related to the biotic and abiotic factors in the three lakes was analyzed. The three lakes have different nutrient contents and levels. The lake at PXPJ is permanently connected with a local river that drains into the lake; thus, it has high nutrient concentration, with an annual average concentration of 0.10 mg/L of total phosphorus (TP) and 1.69 mg/L of total nitrogen (TN). The lake at the PXXQ site has the highest TN concentration of 2.81 mg/L due to seasonal drainage from a local polluted river. The lake at the PXGQ site has the lowest TN concentration of 0.91 mg/L, because it is not connected to any rivers. Moderate amount of phosphorus was detected at the PXGQ and PXXQ sites, with mean values of 0.075 mg/L and 0.045 mg/L, respectively. However, the trophic state index for the three lakes was meso-eutrophic and did not vary considerably across the three lakes. In all, 16 FGs were identified, 11 of which were predominant groups, representing features of typically eutrophic habitats in small lakes. At the PXPJ site, FGs of S1, X2, and Y sites were predominant in spring, with Pseudanabaena sp., Chroomonas caudata Geitler, and Cryptomonas ovata Ehr. as representative species, respectively, whereas C (Cyclotella catenata as a representative) was the first predominant group in summer, autumn, and winter. At the PXGQ site, S1 with Pseudanabaena sp. as a representative was predominant in spring, summer, and autumn, which was then replaced by FGs of C (Cyclotella catenata as a representative) and D (Synedra acus Kützing as a representative). At the PXXQ site, FGs of X2 and Y were the predominant groups in spring, which were succeeded by S1 group in summer and autumn, and then replaced by C (Cyclotella catenata as a representative) and E (Dinobryon bavaricum Imhof as a representative) in winter. Light and temperature were identified as the key environmental factors driving seasonal succession of phytoplankton FGs at the three lakes by using canonical correlation analysis. Nutrient and grazing pressure on phytoplankton could be the main causes for the differences in the community structure among the three sites.