Based on a physical-biological model with monthly mean forcing, numerical experiments are conducted to examine the effects of iron and silicate availability on phytoplankton growth in the equatorial Pacific. The effects of elevated iron are realized in terms of increasing the phytoplankton light acclimation efficiency (α) and decreasing the molar ratio Si/N of diatom uptake. The increase of α (decrease of Si/N) would release the iron stress to phytoplankton growth in the equatorial Pacific thus support higher organic production, which tends to drive the system into nitrate depletion. However, the biogenic silica (BSi) production remains largely unchanged due to the reduction of Si removal for unit production of organic nitrogen by diatoms. As a result, the BSi production is lower than the new production and the Si(OH)4 is higher than the NO3, which is consistent with conditions during glacial periods as inferred from the geological records but opposite to the conditions in the modern equatorial Pacific. The numerical experiments suggest that, if other conditions stay the same, low NO3 concentration during glacial periods may prevent diatoms from out-growing small phytoplankton in the equatorial Pacific.