High optical complexity caused by the variability of marine particles poses a major challenge to the development of bio-optical algorithms for particulate organic carbon (POC) concentration retrievals from optical measurements in coastal waters. Here, we developed a particle composition-specific approach to estimate POC off the coastal areas of Guangdong and eastern Hainan Island, China. The ratio of phytoplankton absorption to detritus absorption coefficient aph(443)/ad(443) was used to optically discriminate water types. The samples with aph(443)/ad(443) ≤ 4.9 showed a significant correlation between POC and absorption line height at 676 nm aLH(676) (R2 = 0.75, n = 70, p < 0.01). In contrast, aph-dominant samples with aph(443)/ad(443) > 4.9 had a high covariance between POC and particle scattering coefficient at 675 nm bp(675) (R2 = 0.85, n = 37, p < 0.01). Validation with an independent dataset yielded a small positive bias (R2 = 0.81, APD = 23.10%, RMSE = 29.01 mg m–3, RPD = 16.31%). The approach provided a better estimation of POC concentration in coastal waters compared with univariate algorithms. A depth-resolved index aLH(676)/bbp(442) was defined as the ratio of absorption line height to particle backscattering coefficient. Using the depth-resolved index instead of aph(443)/ad(443) for optical water type classification can be utilized to represent the vertical variations of POC in 1 m bins, and can complement remote sensing observations to accurately characterize the three-dimensional structure of POC distribution in the oceans.