The photosynthetic pigment composition is an important basis of classification of phytoplankton. Three dimensional (3D) fluorescence spectra of five phytoplankton divisions (Cyanophyta, Chlorophyta, Bacillariophyta, Dinophyta, Cryptophyta) are analyzed and 36 characteristic fluorescence peaks which are related to chlorophyll a, chlorophyll b, chlorophyll c, carotenoid, phycocyanin and phycoerythrin are extracted. On this basis, a classified measurement method of phytoplankton based on characteristic fluorescence of photosynthetic pigments is put forward. Pure cultures and mixed cultures of Microcystis aemginosa, Chlorella vulgaris, Fragilaria sp, Glenodinium gymnodinium and Cryptomonas ovate are tested. For the five pure cultures, the measuring errors are 5.15%, 5.63%, 7.90%, 4.85%, 6.55%. For dominant species (mass fraction higher than 50%), the measuring errors are 7.96%, 8.69%, 5.44%, 10.78%, 15.57%. For subordinate species (mass fraction less than 30%), the measuring errors are 18.29%, 17.52%, 20.01%, 29.11%, 20.14%. The characteristic fluorescence spectrometry is a fast and effective phytoplankton classified measurement method. Its measurement accuracy has reached the level of 3D fluorescence spectrometry, while the data volume and calculation time are only 1.1% and 2.2% of the 3D fluorescence spectrometry.