The South China Sea (SCS), located at the intersection of two major tectonic plates and near the Manila Fault Zone, is a region highly susceptible to earthquakes and tsunami activities. To develop a more comprehensive and reliable understanding of tsunami behaviours over coral reefs, this study employs the actual topography of a coral reef in the SCS and N-wave theory for the numerical simulation, encompassing the entire tsunami life cycle. Utilizing the open-source solver OlaFlow, driven by the Reynolds-averaged Navier-Stokes (RANS) equations, this study performs a series of numerical simulations of N-wave tsunamis considering the measured topography of the coral reef, as well as the real dimension of an engineering defence structure on the top of the coral reef. The adopted tsunami parameters are equivalent to an earthquake with a moment magnitude of 7.1. The simulations focus on the impact of wave profiles and initial static water levels on the propagation and evolution of tsunamis. Numerical simulations reveal that tsunami profiles, water depth, and topography significantly influence the tsunami dynamics, notably in the waveform transformation, the relationship between wave height and trough-to-peak ratio, and the topographic effects on the wave energy dissipation. These results highlight the critical need to incorporate factors such as tsunami profiles, dispersion, and realistic topography into tsunami predictive models for the purpose of more reliable hazard evaluation and the development of effective coastal defences.