This paper used Ulva compressa which is the composing species of green algae communities in Rudong seaweed farming sea area for investigation. Experiments studied the effects of sodium hypochlorite on chlorophyll composition, fluorescence characteristics and photosynthetic rate of U.compressa by chlorophyll extract, chlorophyll fluorescence technology and liquid oxygen electrode. The results showed that with the NaClO concentration increasing, the chlorophyll content and fluorescence characteristics of U.compressa were gradually decreasing. After 10.0 mmol/L NaClO treatment, Chl.a and Chl.b respectively reduced to 0.030 mg/g and 0.039 mg/g; 0.00-6.00 mmol/L NaClO have significant influence on the fluorescence characteristics of the algae; 10.0-100 μmol/L NaClO can make the photosynthetic rate of U.compressa decline significantly in 3 min, in which 100 μmol/L group declined from the control group of 1 315 nmol O₂/(min·g) to -472 nmol O₂/(min·g). According to the experiments and verification in aquaculture area, 4.0 mmol/L NaClO could be regarded as an ideal reagent in green algae removing.