A method for partitioning phytoplankton absorption coefficient is developed in this study using in situ sampling dataset collected from Taihu Lake. Because the absorption of non-algal particles and colored dissolved organic matter(CDOM) has similar optical properties, their absorption coefficients are combined to parameterize by the method. The ratio of phytoplankton absorption coefficient at 580 nm and 692 nm is also used in the method because of its consistence. The performance of the method is assessed both in magnitude and spectral characteristic. The results indicate that the absorption of phytoplankton can be well divided from the total absorption. The method has good performance at band 440, 550 and 675 nm in phytoplankton absorption partition, and the mean relative error is less than 10% at band 675 nm. The phytoplankton absorption spectra partitioned from total spectral absorption keeps its inherent character, and fits with measured ones perfectly, the mean similarity coefficient (SC) of them can reach 0.97.