Concentrations of pigments could reflect the dominant phyla of algae. Investigations of algae in eutrophic lakes revealed that Chl. b, Chl. c and phycobilin (PC) are the critical pigments of chlorophyta, bacilliariphyta and cyanophyta, respectively. In this study, partial least square (PLS) regress was used on the retrieval of Chl. a, Chl. b, Chl. c and PC through absorption spectral of phytoplankton. Retrieve of Chl. a was based on the data collected in situ during 2011. Retrieve of Chl. b and Chl. c was based on the data collected in situ in March, since there is no significant dominant phyla of algae in spring. Result shows that PLS is a more effective method than the original least square regress and could be of help for remote sensing of multi-pigments and the distribution of main algae in eutrophic lakes.