Rapid measurement of phytoplankton photosynthetic parameters is important for bloom and red tide prediction as well as water ecological research. In order to solve the problem of high data sampling rate caused by narrow pulse light source when the fast repetition rate (FRR) method is applied, a phytoplankton photosynthetic parameter measurement system based on variable pulse induced fluorescence is designed. The designed system utilizes a single pulse to realize the single turnover excitation mode, and employs pulse integration to implement weak light pulse signal detection in the relaxation mode. The data sampling rate can be reduced from higher than 10 MS/s to 1 MS/s. The functional absorption cross section of photosystem II (PSII), maximum quantum yield of photochemistry in PSII, and QA- (reduced primary electron acceptor) reoxidation time constant, can be measured rapidly. The relative standard deviation of the three parameters is less than 3%.