Geological records suggest that marine phytoplankton might have arisen in the Proterozoic while zooplankton remained absent, and marine productivity was not excessively low. However, quantitative estimates of phytoplankton biomass and net primary productivity remain elusive. Here, we use the Community Earth System Model version 1.2.2, modifying biological module and boundary conditions, to simulate marine biogeochemical cycles in the Proterozoic. The simulations demonstrate that, within the expected range of nutrient levels, phytoplankton at sea surface was more than 2 times denser than present, sustaining a greener ocean due to the absence of predators. Heavier surface chlorophyll in the Proterozoic would block sunlight from reaching subsurface layers. This so-called self-shielding effect would decrease subsurface net primary productivity significantly. Simulations show that, through the combined influence of low nitrate level under a low-oxygen environment, the absence of diatoms, and self-shielding, the Proterozoic net primary productivity was only approximately 60% and 30% of the present level in warm (almost ice-free) and cold (sea-ice reaches around 30°N/S) periods, respectively. These findings are subject to uncertainties in model framework and Proterozoic nutrients levels; a slightly less green ocean or more productive ocean was possible if the phosphorus level was much lower or higher than the present level.