We have previously shown that the coralline algal assemblages (CAAs) of the South China Sea may indicate post-Pliocene paleo-water depth changes; however, the pre-Pliocene coralline algal compositions and related sea-level significance remain to be elucidated. In the present study, we explore the Miocene coralline algal compositions and their role in recording the sea level, and show the distribution, classification, type, abundance, and diversity of Miocene coralline algae from 213 petrologic thin sections using a coral-reef carbonate sequence from the northern South China Sea. The diversity and abundance of coralline algae in the early and late Miocene are higher than those in the middle Miocene. Eleven genera were identified and grouped into seven CAAs, showing a water depth range from <5 m to >25 m. At 18.67-17.98 Ma, the coral reef was in a stagnation/drowning stage, with rising sea levels exceeding the development of the coral reef. At 17.98-16.78 Ma, the coral reef was in a rapid development during a rapid rise in sea level. Additionally, at 16.78-14.79 Ma, low coralline algal abundance was observed, and the corals were sporadically distributed at a relatively stable sedimentation rate, suggesting a decline in coral reef development. At 14.79-10 Ma, the coral reef development was remarkably slow or stagnant. Furthermore, at 10-5.3 Ma, the coral reefs developed slowly, indicating a gradual rise in the sea level. The sea-level changes indicated by coral reef development are consistent with the long-term global sea-level changes, indicating that the composition and assemblage of Miocene coralline algae can be used to accurately relay the sea-level history.