Biogenic reefs are unique geologic bodies that are the products of biological activity in tropical and subtropical oceans and critical to global carbon cycling. The South China Sea (SCS) has developed largest carbonate platforms in the Western Pacific. The fully-cored Well NK-1, which is drilled through the reef complex on the Meiji Atoll, Nansha Islands, offers good opportunity for assessing the long-term evolutions of biogenic reefs in the SCS. The stratigraphic ages based on palaeomagnetic and Sr isotopic data are controversial in some intervals of core NK-1. To reveal the evolution history of Nansha Islands and their controlling factors, more credible age constraints on core NK-1 are needed. This research presents new records of calcareous microfossils (calcareous nannofossil and foraminifer) abundances and diversities in the biogenic reef carbonates of core NK-1. Based on the assemblages of the calcareous microfossils, seven biostratigraphic datums are recognized from the sequence of core NK-1, revealing a general continuous succession of the earliest Miocene to Pleistocene age. By combining with the magnetostratigraphic data, the development and evolution of carbonate platform in Nansha Islands are reconstructed. The bottom age of the biogenic reef sequence of NK-1 is estimated for 23.03 ± 1.06 Ma, close to the Oligocene/Miocene boundary. The new chronology highlights three short hiatuses of 3.6–2.4 Ma, 11.1–10.0 Ma, and 13.5–11.9 Ma, which are well correlated with the prominent exposed surfaces at 210.3 m, 464.6 m and 561.6 m, respectively. It reveals remarkably similar evolution history of carbonate platforms in the SCS since Neogene by comparing with records of stratigraphy and growth rate from deep drilling cores on isolated coral reefs in Nansha and Xisha Islands. The results showed that the SCS carbonate platform developments, which go through Late Oligocene / Early Miocene initiation phase, Early-Middle Miocene rapid growth phase, Middle-Late Miocene erosion phase, Miocene-Pliocene stable development phase and Quaternary growth phase, are mainly influenced by global sea level changes, environmental factors and regional tectonism such as the SCS basin spreading, Sabah Orogeny Movement and Dongsha Movement.