From January 2008 to December 2009, phytoplankton and its related influenced factors were monitored for 1 time/a month in Xinanjiang Reservoir. A total of 103 taxa were identified by microscope during the two years. The phytoplankton density was ranged from 1.46×10⁶ cells/L to 2.55×10⁷ cells/L, with an average value of 6.09×10⁶ cells/L. Two peaks of the phytoplankton density values appeared in spring and autumn. The specific composition of phytoplankton community was varied with seasons. Phytoplankton community was dominated by Bacillariophyta and Cryptophyta in spring and winter. However, the dominated species of the phytoplankton community were Cyanophyta and Chlorophyta in summer; phytoplankton in autumn was dominated by Cyanophyta and Bacillariophyta. It is found that phytoplankton density is significantly positively correlated with total phosphorus, chla and the last month precipitation, notably negatively relevant to transparency, and no obvious relevance with total nitrogen(TN). Seasonal variability in the hydrology situation of reservoir can significantly affected the phytoplankton structure and the density of the seasonal changes and short-term phytoplankton growth is obviously dual-effected by the river basin water and temperatures. From the view of large scale ecological effect, it is thought that the top-down effect of food web was the dominant factor of phytoplankton density in Xin'anjiang Reservoir at present. Mass filter feeding omnivorous fish dropped to zooplankton caused higher predation pressure, which indirectly promotes the phytoplankton population growth. In nitrogen and phosphorus nutrient respect, phosphorus was a key factor. So keeping low phosphorus concentration and ratio of N/P more than 100 to reduce the phytoplankton density has realistic meanings.