The monsoon system modulates surface production in the South China Sea (SCS). The winter monsoon has long been recognized as the primary factor regulating surface production in the northern SCS; however, the role of monsoon remains in debate in the southern SCS. Here, we present a long record of short-chain n-fatty acids (n-FAs) in reefal carbonates from one deep well (NK1) on an isolated coral atoll (Meiji) in order to provide new insights into the change of surface production in the southern SCS since the Late Miocene (ca. 10.5 Ma). Short-chain n-FAs indicative of total marine organic matter input are rather feasible to reflect the total production associated with mixotrophic reef-building corals that feed on various marine biotas (i.e., phytoplankton, zooplankton and bacteria). By ruling out the significant influence of diagenetic and degradation processes, short-chain n-FAs can be further applied to reconstruct paleo-production in Well NK1 coral reefs. The temporal distribution of short-chain n-FAs changes similarly with many other independent paleo-production records (i.e., Ln(Ba/Ti) and opal) in Well NK1 and adjacent ODP Site 1143, demonstrating the close coupling between coral reef production and surface water production. This occurs through the common factor of nutrients in modulating production of symbiotic autotrophic coralgae and asymbiotic phytoplankton and/or the large heterotrophic dependence of corals on phytoplankton-governed food webs in surface waters. Short-chain n-FAs inferred surface production displays a progressively decreased trend from the Late Miocene to Pliocene (ca. 10.5–2.6 Ma) followed by a substantial increase since the Pleistocene on million-year timescales, which follows the variation of terrigenous supply to the coral atoll and responds almost inversely to the sea-level change. Accordingly, we propose that long-term paleo-production in the southern SCS was associated with terrestrial nutrient input which was controlled by relative sea-level change since the Late Miocene. This study highlights the feasibility of short-chain n-FAs as appropriate production recorders in shallow-water coral reefs which are widespread in tropical-subtropical oceans, providing valuable perspectives on long-term paleo-production evolution in surface waters.