Aquaculture in large water bodies has become an important culture mode of Litopenaeus vannamei in coastal waters. Fractionated chlorophyll-a (Chl-a) and environmental factors of the large water ponds with high salinity (54, n=3) and the control ponds (32, n=3) were investigated from May to July 2020 to explore the variations in Chl-a, phytoplankton particle size, and the response to environmental factors during the aquaculture season. Pearson correlation analysis was performed to analyze the relationship between the environmental factors and the size-fractionated Chl-a concentration. Partial redundancy analysis (RDA) was applied to assess the effects of environmental factors (including silicate, active phosphate, ammonia salt, nitrite, nitrate, water temperature, salinity, dissolved organic nitrogen, and dissolved organophosphorus) on total Chl-a, Chl-a of micro phytoplankton (micro Chl-a), Chl-a of nano phytoplankton (nano Chl-a), and Chl-a of pico phytoplankton (pico Chl-a). The following results were obtained:1) Diurnal variation of Chl-a: Total Chl-a of the high-salinity group showed no significant diurnal variation (P > 0.05). Total Chl-a of the control group showed significant diurnal change in May and June (P < 0.05). The highest value of total Chl-a in May occurred at 15:00, while the highest value of that in June was at 08:00. For size-fractionated Chl-a, pico Chl-a in the high-salinity group showed significant diurnal variation in July (P < 0.05), with the highest value appearing at 12:00. Micro Chl-a in the control group showed significant diurnal changes in May, June, and July (P < 0.05), and nano Chl-a in the control group showed significant diurnal changes in June (P < 0.05).2) Monthly changes of Chl-a: The lowest and highest values of total Chl-a occurred in June and July, respectively. Total Chl-a in July was significantly higher than that in May and June (P < 0.05). For size-fractionated Chl-a, the pico Chl-a and nano Chl-a of the high-salinity group in July were significantly higher than those in May and June (P < 0.05) and showed no significant difference between May and June (P > 0.05). Pico Chl-a, nano Chl-a, and micro Chl-a of the control group in July were significantly higher than those in May and June (P < 0.05) and showed no significant difference between May and June (P > 0.05).3) Contribution of size-fractionated phytoplankton in high-salinity and control groups: The contribution of micro Chl-a, nano Chl-a, and pico Chl-a to total Chl-a in the high-salinity group were (15.64±0.16)%, (73.81±0.13)%, and (10.55±0.06)%, respectively. Nano Chl-a was dominant in May, June, and July. The contribution of pico Chl-a increased from 6.43% in May to 16.81% in July, and exceeded that of micro Chl-a. The contributions of micro Chl-a, nano Chl-a, and pico Chl-a to total Chl-a in the control group were (52.29±0.10)%, (41.82±0.10)%, and (5.59±0.01)%, respectively. Micro Chl-a concentration had a major advantage in May and June, accounting for 59.64% and 57.49%, respectively. Nano Chl-a concentration accounted for 35.46% and 36.90%, respectively. By July, nano Chl-a had a major advantage, contributing to 53.09%.4) Pearson correlation analysis showed no significant correlation between the diurnal variation of Chl-a and the environmental factors of the high-salinity group in May and June (P < 0.05). Yet, the concentrations of nano Chl-a and total Chl-a were negatively correlated with the concentration of nitrate in July (P < 0.05). The concentrations of micro Chl-a and total Chl-a were positively correlated with those of silicate (P < 0.05). For the control group, Pearson correlation analysis showed a significant positive correlation between nano Chl-a and water temperature (P < 0.05). Total Chl-a and phosphate were negatively correlated in May (P < 0.05). There was a significant negative correlation between pico Chl-a and nitrate in July (P < 0.05).5) For the high-salinity group, RDA revealed a significant positive correlation between Chl-a and water temperature, and the contribution of nano Chl-a increased with the increase in temperature. Total Chl-a was positively correlated with silicate and negatively correlated with phosphate, dissolved organic nitrogen, and dissolved organophosphorus in the high-salinity group. For the control group, RDA showed that total Chl-a was positively correlated with dissolved organic nitrogen and negatively correlated with silicate and nitrite. In general, Chl-a in high-salinity ponds has a small diurnal variation, and the phytoplankton particle size gradually decreased with cultivation, which may be caused by the increasing temperature and high organic nitrogen concentration.