Xiquanyan Reservoir, as the second water source place of Harbin, whose water ecosystem's state of health needs to be monitored effectively. In this study, the reservoir and upper rivers were sampled at 13 points, 9 of which were in the reservoir area and the others in the inflow-river area. In July and August of 2010, the phytoplankton were both qualitative and quantitative studied, along with the investigation on the water environmental factors. The results showed that, in total,7 phyla 169 species were identified, the majority of which were Chlorphyta(83 species), Bacillaroiphyta(47 species) and Cyanophyta(15 species). The others were listed as Euglenophyta(12 species), Chrysophyta(6 species), Pyrrophyta(4 species) and Cryptophyta(2 species). In summer, the phytoplankton abundance and biomass were 10.92×10⁵-88.44×10⁵ cells/L(the mean value is 51.6×10⁵ cells/L) and 2.61-22.44mg/L(the mean value is 10.37mg/L), respectively. The Shannon-Wiener index was between 2.46-4.69 with the mean value of 3.33. Moreover, Cyclotella meneghiniana, Synedra ulna, Phormidium allorgei and Planctonema sp. were the key dominant species in summer.Canonical correspondence analysis was used to analysis the phytoplankton community structure and their relationship with environmental factors. The results showed that, 1) The phytoplankton community in different sampling sites reflected significant spatial and temporal heterogeneity; 2) The estuary area, lake central district and the dam area were of significant difference, and the river water quality was significantly better than that in reservoir area; 3) Ammonia, nitrate, total nitrogen and total phosphorus were the main driving factors of phytoplankton populations. This study suggested that, the Xiquanyan Reservoir water body has been in moderate eutrophication level, and there is a risk of further eutrophication. Therefore, we proposed reservoir management departments to establish the system of ecosystem health monitoring, assessing and early-warning, to ensure the safety of Harbin water supply.