Internal tides (ITs) are ubiquitous in the stratified ocean and are known to significantly influence the physical and chemical properties of water masses, especially in oligotrophic regions. However, the mechanisms by which ITs enhance chlorophyll concentrations through physical–biogeochemical interactions remain insufficiently understood. To investigate IT‐driven biogeochemical processes in the northern South China Sea (SCS), a coupled physical‐biogeochemical model was developed by integrating the CoSiNE biogeochemical module with the fully nonhydrostatic MITgcm (MIT general circulation model). The model is evaluated via comparisons with in situ observations. Numerical simulations reveal contrasting biogeochemical responses to ITs. In IT‐unaffected regions, nutrient concentrations in the euphotic zone remain stable, whereas IT passage induces a rapid elevation of nutrient levels by up to 30%, with elevated concentrations persisting for a minimum of 6 hr. Spatially, intense chlorophyll patches emerge in close alignment with IT crests, exhibiting depth‐integrated chlorophyll increases of approximately 40%. Moreover, despite similar nutrient changes across the diel cycle, high chlorophyll concentrations occur about 4–6 hr after the IT trough passes during daytime due to the growth of phytoplankton, contributing approximately 20% of net phytoplankton growth. Chlorophyll budget analysis further reveals that the increase in chlorophyll arises from immediate physical transport and delayed physiological responses. These findings underscore the essential role of ITs in modulating nutrient availability and primary productivity in the oligotrophic oceans, thereby offering insights into primary production and carbon cycling processes in nutrient‐limited marine ecosystems.