Hongfeng Reservoir is located at Guizhou Province, which has the most widely distributed and the most complex types of karst. The reservoir is one of the sources for drinking water for Guiyang city. Besides, it has many other functions, such as agricultural irrigation, flood control, and tourism. Management of the eco-environment and water resources of this reservoir are important for sustainable development of this area. This study identified functional groups of phytoplankton to understand the distribution patterns of the Hongfeng Reservoir, which is different from the traditional approach of community identification. Phytoplankton and water samples were collected in dry period (November 2012), level period (April 2013), and flood period (July 2013). In total, 25 functional groups of phytoplankton were identified, wherein, the groups S1, F, J, B, D, S2, Y, and L_M were comparatively common functional groups, and the groups W1, A, W2, K, and X3 were less common. Habitat characteristics of the main functional groups that are adapted to the eutrophication of water bodies included codon S1 habitat template: turbid mixed environments, codon F habitat template: clear, deeply mixed meso-eutrophic lakes, codon J habitat template: shallow, mixed, highly enriched systems (including many low-gradient rivers), codon B habitat template: mesotrophic small- and medium-sized lakes with species sensitive to the onset of stratification. The seasonal changes among the three sampling sites were generally the same. During dry period and level period of phytoplankton functional groups of each site is less, the plentiful functional group of the largest number in the wet period. The dry period, level period, and wet period have 16, 19, and 22 function groups, respectively. The main representative functional groups are J/B/P for dry period, S1/J/B/F for average water season, and S1 (dominant functional group)/D/J for wet period. Phytoplankton functional groups changed at depth of 6 m for Jiangjunwan and Houwu, and at depth of 10 m for Dam. In addition, the analysis of changes in the environmental factors suggested that water nutrient is no longer the limiting factor for the phytoplankton growth, and that water temperature is the most important factor influencing the spatial and temporal distribution of the phytoplankton functional groups. The strategy of the phytoplankton growth followed the law: CR/R/S in dry period→R/CR/CS in level period→R/CR/CRS/C in wet period(C means Competitors; R means Ruderals; S means Stress-tolerators). Phytoplankton functional groups can grow well under ideal conditions of material supply and energy input. The phytoplankton functional groups increased with the increase in the degree of energy restriction and were more tolerant than other groups. It could be concluded that Hongfeng Reservoir is in the meso-eutrophic state based on the correlation of phytoplankton functional groups and aquatic environment.