We studied 344 samples from Well XK-1 in Xisha Islands, South China Sea, and identified 66 species of larger benthic foraminifera, providing critical evidence for biostratigraphy and palaeoenvironmental interpretation of the Miocene reef carbonate sequence. Three assemblages are recognized, namely, Spiroclypeus higginsi–Borelis pygmaeus Assemblage (Letter Stage Te5, Early Miocene, 1256.28–1180.15m), Nephrolepidina–Miogypsina Assemblage (Tf, Middle Miocene, 1031.10–577.04m), and Cycloclypeus–Heterostegina Assemblage (Tg, Late Miocene, 468.13–380.42m). On the basis of the palaeoecological preference of the larger foraminifera, we interpret that the Miocene carbonate sequence was deposited mainly in a warm tropical shallow water environment, characterized by five stages of continuous long-term evolution: backreef lagoon to shelf in the Early Miocene, normal to frontal reef in the early Middle Miocene, backreef lagoon to shelf in the later Middle Miocene, normal to frontal reef in the early Late Miocene, and proximal forereef shelf in the later Late Miocene.