This study employs Coupled Model Intercomparison Project Phase 6 Earth System Models under Shared Socioeconomic Pathways (SSPs) scenarios SSP2-4.5, SSP3-7.0, and SSP5-8.5 to investigate the future projection of biogeochemical conditions in the southern South China Sea (SCS) from 2015 to 2100. We focus on projected changes in Sea Surface Temperature and seven important biogeochemical variables such as Chlorophyll, Phytoplankton, integrated Primary Production, Oxygen, Nitrate, Phosphate and pH. Our results consistently indicate substantial warming of +1 to +3 °C at the end of 21st century across all scenarios in southern SCS region, potentially leading to cascading consequences for marine ecosystems and fisheries. Projected increases in surface temperatures are expected to induce declining dissolved Oxygen levels of -3 to -8 mmol m-3 and ocean acidification of -0.1 to -0.4 units, posing a multifaceted threat to this crucial fishing ground. Furthermore, our analysis suggests a significant decrease in Phosphate concentrations ranging -1.4 to -2 mmol m-3/year across all scenarios. This decline in nutrient availability could potentially limit productivity and the entire marine food web in this region. These projections provide valuable scientific insights for policymakers and stakeholders to formulate strategies aimed at mitigating the adverse effects of climate change on the southern SCS and ensuring the long-term sustainability of its fishery resources.