Chlorophyll-a concentration is usually measured to indicate algae biomass and to evaluate eutrophication level of freshwater lakes. Based on the water quality monitoring data from December 2012 to November 2013, this paper is aimed to analyze the spatial-temporal variation characteristic of chlorophyll-a concentration in Lake Hongze and further to explore the relationship of chlorophyll-a concentration and other water quality factors. Firstly, from the statistical charts of series chlorophyll-a concentration from eight water sampling sites, the seasonal variation curve of eastern zone showed a bimodal in about March and August. However, the seasonal variation curve of chlorophyll-a concentration in the northern zone and western zone were different. The tendency of chlorophyll-a concentration in above two zones kept steady in spring, decreased in middle of summer and then increased to the summit in about September. There were significant differences among three zones in spring and winter, meanwhile, the difference of chlorophyll-a concentration in other two seasons was not significant. In spring and winter, the chlorophyll-a concentration in eastern zone was apparently lower than that of the other two zones, which was mainly due to its high liquidity and the frequent movement of lake currents. Moreover, because of a large amount of nutrients from the surrounding farmland and fish pond injecting into the southern zone, the chlorophyll-a concentration in this zone was much higher than that of other zones. Finally, the canonical correspondence analysis between chlorophyll-a concentration and aquatic factors, including chemical oxygen demand, dissolved oxygen, total phosphorus, total nitrogen and temperature, was applied in the present research. The results revealed different response relationship existed in different months and locations. Therefore, reducing the polluted inflow from upstream, farm and fish pond was probably effective way to control algae biomass in Lake Hongze.