Abstract: Ordination has been widely used in analyzing bio-community dynamics. Based on the survey data of Qinshui River, the non-metric multidimensional scaling(NMDS) method was used in analyzing phytoplankton community dynamics and its driving factors. BIO-CORDs were laid out in the Qinshui River in June, 2014, in order to intercept surface runoff and various pollutants therein flowing into Lake Taihu. Water quality was monitored simultaneously during the period from June to December, 2014. The monitoring data were cited in exploring applicability of the NMDS to analysis of phytoplankton community structure. Results of the analysis show that at the initial stage of the BIO-CORD operation TN and TP dropped significantly in concentration(P<0.01). However, at the late stage, the effect of BIO-CORD was not so significant. Results of NMDS show that the phytoplankton community in the water treated with BIO-CORD did not vary much from the control throughout the period, except for June and October, which indicates that varying temperature due to season alternation is the key factor that triggers the succession of phytoplankton community. All the findings in this experiment also illustrate that NMDS is a useful tool in analyzing phytoplankton community.