From September 2012 to June 2013, phytoplankton surveys were conducted in the outer and outer tidal zones of the north branch of the Yangtze River estuary. A total of 228 species of 75 genera of phytoplankton were identified, including 153 species of Bacillariophyta, 25 species of Chlorophyta, 21 species of Cyanobacteria, 14 species of Dinoflagellates, 2 species of Chrysophyta, 2 species of Xanthophyta, 2 species of Cryptophyta and 9 species of Euglena.There was obvious seasonal variation in the species composition of phytoplankton. There are 73 species of 31 genera and 6 phyla in spring, 106 species of 34 genera and 5 phyla in summer, 111 species of 61 genera and 7 phyla in autumn, and 63 species of 27 genera and 5 phyla in winter. The abundance of each season was 3.78×10⁵ cells/L in spring, 7.93×10⁵ cells/L in summer, 3.72×10⁵ cells/L in autumn, and 1.14×10⁵ cells/L in winter. The CCA model response analysis of phytoplankton and hydration factors was carried out. The results showed that suspended solids, turbidity and nutrient salt had great influence on the abundance of phytoplankton. Due to the change of shellfish and environmental factors, the composition of phytoplankton changed significantly before and after ecological restoration. The number and abundance of phytoplankton increased obviously in all seasons.