Cnoidal waves are capable of effectively characterizing wave motion in shallow water regions, holding significant practical value for the precise description of nearshore hydrodynamic processes. To investigate the propagation and evolution patterns of cnoidal waves across typical reef-lagoon systems, this study conducted physical model experiments in wave flumes, with focused analysis on the influences of incident wave height, reef flat submergence, and wave period on wave nonlinear characteristics, energy dissipation, and hydrodynamic parameters. The results demonstrate that reef topography substantially enhances wave nonlinearity, with conspicuous waveform steepening in the fore-reef slope zone and sawtooth-shaped wave profiles accompanied by phase lag over reef flats. Increased incident wave height induces stronger nonlinear effects, promoting higher harmonic growth and significantly enhancing wave setup and run-up, while reducing reflection coefficients due to enhanced transmission. However, greater reef flat submergence weakens nonlinear wave effects and causes a monotonic decrease in reflection coefficients. Under deeper water conditions, vertical momentum flux intensifies, and run-up exhibits nonlinear growth. The influence of wave period manifests complex patterns: maximum wave energy concentration and the most pronounced higher harmonics occur at T=2.25 s. Short-period waves (T<2.25s) experience intensified shoaling deformation that aggravates waveform distortion, whereas long-period waves (T>2.25 s) exhibit characteristic attenuation through energy dissipation. This research provides critical experimental evidence for coral reef ecosystem conservation and coastal engineering design.