The South China Sea (SCS) is characterized by strongly stratified, oligotrophic surface water, which leads to pronounced vertical gradients in biogeochemical properties. Understanding how these conditions shape organic carbon dynamics provides an instructive analogue for elucidating carbon cycling in the vast subtropical oceans. During the sharing cruise of the SCS basin, suspended particles were collected, and compound-specific δ¹³C values of individual amino acids and fatty acids were measured. Distinct isotopic gradients were observed across individual compounds. By applying a genetic algorithm (GA), we developed a parameter optimization model that quantifies the abundance of individual compounds derived from phytoplankton, bacteria, and exported particulate organic matter (POM) from the upper water column. The identification of changing source compositions across individual compounds suggests that POM compounds exhibit distinct geochemical behaviors according to their varying reactivities. Accordingly, we propose a mechanistic model that describes the biogeochemical cycling of POM across a full spectrum of reactivities.