The structure of phytoplankton community was investigated based on morphological identification and high-throughput sequencing in the Nan’ao waters in May 2022. The spatial distribution of phytoplankton in relation to environmental factors was explored and results from two different methods were also compared and discussed. According to the cluster analysis of environmental factors, the survey area can be divided into nearshore area and offshore area. Totally, 105 species belong to 52 genera, 39 families, 27 orders, 8 orders, 5 phyla were morphological identified, while 543 species in 6 phyla, 32 orders, 97 families, 155 families, 272 genera through high-throughput sequencing were identified. Bacillariophyta and Dinophyta were the main groups, composing 74.54% and 24.78% through microscopic identification, and 17.52% and 67.84% through high-throughput sequencing, respectively. The abundance of phytoplankton identified by morphology ranged from 0.11×10⁵ to 6.85×10⁵ cells·L^-1, which was significantly correlated with the distribution of chlorophyll a concentration, and the phytoplankton diversity index was lower than that of the high-throughput sequencing method. 7 dominant species were obtained by both methods, of which the absolutely dominant specie in the morphological identification results was Chaetoceros compressus, and the absolute dominant specie in the high-throughput sequencing identification results was Heterocapsa rotundata. Correlation analysis showed that the main environmental factor affecting phytoplankton community structure in Nan’ao in spring was pH, salinity and DIP (dissolved inorganic phosphorus). Using the combination of morphological identification and high-throughput sequencing technology, the structure and diversity of the phytoplankton community can be described more comprehensively and accurately.