This study is based on phytoplankton field data collected in August 2023 from the suspended mussel farms of Gouqi Island, Zhejiang Province, using the underwater digital holographic particle imaging system (Lisst holo2) and traditional net sampling combined with microscopy. A comprehensive comparative analysis of particle imaging data and net sampling data was conducted, with a focus on diurnal variations in phytoplankton community structure and influencing factors. During the survey, 75 phytoplankton species belonging to 38 genera and 5 phyla were identified, with dominant species including Noctiluca scintillans and Rhizosolenia styliformis.Significant diurnal variations in phytoplankton species richness and abundance were observed. At midday, most phytoplankton migrated toward deeper layers, resulting in significantly higher species numbers and abundance in the bottom layer compared to the surface. By evening, differences between surface and bottom layers diminished, with a vertical migration pattern dominated by dinoflagellates (primarily Noctiluca scintillans), characterized by daytime descent and nighttime ascent. Phytoplankton abundance exhibited a moderate correlation with tidal cycles, showing a notable increase during flood tide within the aquaculture water layer. The study area displayed a transition from diatom-dominated blooms to Noctiluca scintillans-dominated blooms.Phytoplankton co-occurrence network analysis revealed that the aquaculture layer had fewer species and lower abundance compared to the whole water column. However, its network complexity (186 edges) was higher, indicating stronger community stability and more intensive species interactions (e.g., mutualism or competition) within the aquaculture layer. Compared to traditional sampling methods, Lisst holo2 addresses limitations such as cumbersome sample preservation and processing, delayed data acquisition, and challenges in measuring phytoplankton particle size. This study validates its reliability in monitoring large-sized algae (e.g., Noctiluca scintillans), highlighting its potential for future marine ecosystem monitoring and conservation research.