Knowledge of phytoplankton community structures is important to the understanding of various marine biogeochemical processes and ecosystem. Fluorescence excitation spectra (F(λ)) provide great potential for studying phytoplankton communities because their spectral variability depends on changes in the pigment compositions related to distinct phytoplankton groups. Commercial spectrofluorometers have been developed to analyze phytoplankton communities by measuring the field F(λ), but estimations using the default methods are not always accurate because of their strong dependence on norm spectra, which are obtained by culturing pure algae of a given group and are assumed to be constant. In this study, we proposed a novel approach for estimating the chlorophyll a (Chl a) fractions of brown algae, cyanobacteria, green algae and cryptophytes based on a data set collected in the East China Sea (ECS) and the Tsushima Strait (TS), with concurrent measurements of in vivo F(λ) and phytoplankton communities derived from pigments analysis. The new approach blends various statistical features by computing the band ratios and continuum-removed spectra of F(λ) without requiring a priori knowledge of the norm spectra. The model evaluations indicate that our approach yields good estimations of the Chl a fractions, with root-mean-square errors of 0.117, 0.078, 0.072 and 0.060 for brown algae, cyanobacteria, green algae and cryptophytes, respectively. The statistical analysis shows that the models are generally robust to uncertainty in F(λ). We recommend using a site-specific model for more accurate estimations. To develop a site-specific model in the ECS and TS, approximately 26 samples are sufficient for using our approach, but this conclusion needs to be validated in additional regions. Overall, our approach provides a useful technical basis for estimating phytoplankton communities from measurements of F(λ).