In recent years, algae bloom is common in the flowing waters, which has been one of the top scientific problems after the algae bloom in lakes. Due to the water pollution, phytoplankton blooms arose in Qinhuai River between August and September, 2010. Based on the conventional monitoring data in August 15 and September 8, 2010, this paper studied the spatial distribution characteristic of chlorophyll-a and its relationships with environmental factors. Results showed that chlorophyll-a concentration appeared obvious spatial difference from upstream to downstream, with a mean value of 73.7 μg/L and the maximum value occurred in Mamuqiao(184.52 μg/L). The ratio of TN/TP was 26.86, and the logarithmic correlation between chlorophyll-a and TP was positive, but the logarithmic correlation between chlorophyll-a and the TN/TP ratio was negative. It suggested that phosphorous might be the main impact factor for blue-green algae. Significantly positive correlation was found between chlorophyll-a and pH and DO, and significantly positive correlation was found between chlorophyll-a and NO₂^--N, but no significant correlation between chlorophyll-a and NH₄⁺-N, NO₃^--N and TN.