The sea surface microlayer (SML) is the thin boundary layer between the ocean and the atmosphere. Phytoplankton community in the SML is known as phytoneuston and has a different community structure and biomass from the phytoplankton of the underlying bulk water. In this study, water samples were collected from the SML of Daya Bay in southern China in September, October, and December of 2013. Algal growth potential (AGP) tests were conducted by adding different forms of nitrogen ( N), phosphorus (P) and silicate (Si). Phytoneuston grew well with both inorganic and organic nutrients, and showed comparable community structure after nutrient addition. A total of 16 pigments were analyzed in the SML samples collected from Daya Bay in this study. Phytopigments were dominated by the cyanobacteria-diagnostic pigment (zeaxanthin, Zea) in September and October, and by diatom- diagnostic pigment (fucoxanthin, Fuco) in December. The concentrations and proportions of Fuco increased greatly after the nutrient addition, and the concentrations and proportions of Zea decreased accordingly. Additionally, the diatom pigment index (DiatDP) increased after nutrient addition, and the prokaryotic pigment index (ProkDP) conversely decreased. The results suggested that massive occurrences of Zea and cyanobacteria are important characteristics of phytoneuston structure in Daya Bay especially in warm seasons, and nutrient addition especially Si addition promoted the growth of diatoms.