Phytoplankton is one of the major primary producers in aquatic ecosystems, and plays a critical role in the normal functioning of aquatic ecosystems by providing material and energy. Changes in the aquatic ecological environment can affect phytoplankton abundance and community structure, leading to the occurrence of harmful algal blooms. In this study, the trends in temporal variation and seasonal characteristics of nutrient concentrations (including total nitrogen, ammonium, nitrate, and total phosphorus), phytoplankton abundance (including Cyanophyta, Chlorophyta, Bacillariophyta, etc.), as well as phytoplankton community structure were analyzed, using continuous monthly monitoring data of four sampling sites located in Zhushan Bay and West Coast of Lake Taihu between 2003 and 2012. Relationships between phytoplankton abundance and water temperature coupled with nitrogen and phosphorus were evaluated simultaneously. The results showed that the concentrations of nitrogen and phosphorous generally decreased during the ten years; this was particularly apparent for the concentrations of total nitrogen (from 7.30 mg/L to 4.25 mg/L) and ammonium (from 4.19 mg/L to 0.81 mg/L) at Zhushan Bay, and nitrate concentration (from 2.01 mg/L to 0.75 mg/L) at West Coast of Lake Taihu. In contrast, phytoplankton abundance generally increased, with the maximum annual phytoplankton abundance of 5293.2×10⁴ cells/L and 3802.8×10⁴ cells/L observed in 2012, at Zhushan Bay and West Coast of Lake Taihu, respectively. Cyanobacteria became the absolutely dominant species, constituting 90.4% and 87.5% of the total phytoplankton community in 2012 at Zhushan Bay and West Coast of Lake Taihu, respectively. Additionally, nitrogen concentrations were higher in spring and winter than in the other two seasons, whereas total phosphorous concentrations and phytoplankton abundance showed the opposite seasonal trends. Pearson's correlation analysis indicated that cyanobacterial abundance and its percentage in the total phytoplankton community were positively correlated with water temperature (r=0.474, P < 0.01), and negatively correlated with ammonium concentration (r=-0.432, P < 0.01) and TN/TP ratio (r=-0.450, P < 0.01). Under the effects of both temperature and nutrient structure, gradual cyanobacterial blooms occurred earlier but disappeared later, thus, leading to the increased duration of cyanobacterial blooms in Zhushan Bay and West Coast of Lake Taihu during 2003-2012. With the increased deleterious effects of global warming, more stringent nitrogen and phosphorus limiting thresholds are required to control cyanobacterial blooms in Lake Taihu. Furthermore, phosphorus remains the critical nutrient that must be controlled in the heavily polluted northwestern Lake Taihu.