Modelling vertical changes of size-fractionated phytoplankton primary production (PP) offers a holistic route to describe marine ecosystems and constitutes an important part of remote sensing to accurately estimate the depth- integrated PP in the global oceans. However, there is no size-fractionated PP model established in the Northern South China Sea (NSCS) yet. In situ measured hyperspectral absorption and irradiance data were used to estimate vertical size-fractionated PP. Results demonstrated that the estimated size-fractionated PP showed good agree- ment with in-situ measurement. r2s are 0.41, 0.69, and 0.83, and median absolute percentage difference are 23.33%, 25.86%, and 31.05% for pico-, nano-, and micro-PP, respectively. The intercept from the linear rela- tionship between ratio of phytoplankton absorption coefficient (aph(435)/aph(676)) and quantum yield of photosynthesis have the biggest impact on estimation of PP based on Monte Carlo approach. The model derived PP profiles showed an exponential attenuation shape curve from the surface to the bottom in coastal water of NSCS. In contrast, a decreasing pattern with increasing depth with a maximum in the subsurface layer or at the chlorophyll maximum depth was observed in the open ocean of NSCS. Such an approach can be utilized to depict the vertical variations of size-fractionated PP, which can serve as supplementary of remote sense to reveal their three-dimensional structure.