The packaging effect of phytoplankton pigments is sometimes capable of accounting for over half of the variability in the phytoplankton absorption coefficient (aph) in oceanic waters. Given the significance of aph in many marine biogeochemical and environmental processes, exploring the packaging effect on absorption properties thus becomes a crucial task. In the present study, two pigment compensation models for quantifying the packaging effect are developed for Case I and Case II waters, respectively, based on high-performance liquid chromatography (HPLC)-derived pigments and aph data from the NOMAD and the marginal seas of China. As a critical quantity in developing our models, phytoplankton “missing” absorption is derived by subtracting the reconstructed aph without the packaging effect from the measured aph. Our proposed models use the established relationships between “missing” absorption and specific absorption coefficients of pigment groups without the packaging effect to quantify pigment group concentrations. Validation using independent in situ data sets demonstrates that great improvements are achieved for the quantification of the packaging effect, especially for waters under abnormal packaging effect conditions. Applying the proposed models to satellite data displays the spatial distributions of the packaging effect in the Atlantic Ocean and the marginal seas of China, as delegates of Case I and II waters, respectively. The generated spatial distribution demonstrates a rule that the packaging effect intensity positively covaries with chlorophyll-a distribution. The findings of this study exhibit a capability of mapping a spatial distribution of the packaging effect from satellite observations for the first time.