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The gas hydrate deposit in Shenhu, Northern South China Sea (NSCS) was one of the main sources for deep-water hydrocarbon and hydrate. Based on field observations on a gas hydrate deposit among 20 × 20 km2 at Shenhu of the northern continental slope of SCS in May (before drilling) and September (after drilling) in 2015, environmental baseline, comparisons of phytoplankton community, biomass and potential environmental drivers were studied. Results indicated the deposit area was a typical low-nutrients low-chlorophyll a (LNLC) environment, characterized by low phytoplankton abundance and diversity. The maximum of abundance and Chl a were fixed at 75 m before and after drilling, but their decrease was larger from 0.53 mg/m3 to 0.40 mg/m3 and 1218 cells/L to 843 cells/L with non-significance found, respectively. After drilling, ammonium decreased significantly (2.13 μmol/L to 0.20 μmol/L), along with nitrite, salinity and dissolved methane, while pH increased significantly (8.10–8.19). Phytoplankton community was composed of 97 taxa of 47 genera in 4 classes, including diatoms, dinoflagellates, cyanobacteria and chrysophyte. The dominant diatom species before and after drilling remained the same, which included Navicula parva , Pseudonitzchia circumpora and Fragilariopsis doliolus. Dominant dinoflagellates shifted from the cosmopolitan Scrippsiella trochoidea to the warm-water adapted Gyrodinium flavum. The diazotrophic cyanobacterium Trichodesmium thiebaultii become more apparent in higher occurrence and abundance due to alleviation from lower-pH inhibition on nitrogen fixation. Redundancy analysis and Spearman correlation analysis revealed that the dominant species and Chl a were mainly associated to pH, DO and nitrite. The X-bar control chart indicated that a constrained maximum problem of phytoplankton abundance in particular layers (50 m, 75 m and 100 m). We clearly documented in the revisited stations (SH3–W2 and SH3–W14), the decrease of abundance and Chl a and the increase of pH and DO were evident in each sampling layer accompanied with lower dissolved methane associated to in situ anoxic or aerobic microniches activities, but the correlations with dissolved methane were not strong. • The gas hydrate deposit in Shenhu, NSCS was a typical low-nutrients low-chlorophyll environment accompanied with low phytoplankton abundance and diversity • Nitrite, pH and DO were major factors causing phytoplankton fluctuation, while dissolved methane had non-significant impact directly. • Variation of subsurface methane was likely resulted from in situ anoxic or aerobic microniches activities. [ABSTRACT FROM AUTHOR]