Abstract: Waves propagating shoreward into the shallow-water zone of a reef become markedly more nonlinear, and the classical Stokes and linear wave theories can no longer describe their deformation accurately. Physical model experiments were therefore conducted in a wave flume to investigate the propagation and transformation of cnoidal waves over a compound-slope reef topography, and to examine the effects of incident wave height, wave period and water depth on the wave hydrodynamics. The compound-slope topography strongly controls the evolution of these nonlinear long waves and the associated wave setup: the cnoidal waves shoaled continuously and leaned progressively forward while climbing the fore-reef slope, and after breaking near the reef edge the energy at the peak frequency decayed rapidly while the low-frequency long-wave energy grew across the reef flat. Under the reference condition (H₀ = 0.06 m, T = 2.50 s, h = 0.506 m), the mean wave height increased to a maximum of 1.28 times the incident wave height, and the free-surface oscillation at the shoreward end of the reef flat was about 73% lower than that of the incident wave. As the incident wave height increased from 0.04 to 0.10 m, the normalized breaking wave height and the transmission coefficient decreased, the maximum reef-flat setup and the maximum run-up on the rear slope rose from 0.118 to 0.325 m and from 0.088 to 0.177 m, and the reflection coefficient varied non-monotonically, first decreasing and then increasing. As the wave period increased, the normalized breaking wave height, the transmission coefficient, the reef-flat setup and the rear-slope run-up generally increased, whereas the reflection coefficient fluctuated locally owing to the phase difference between the incident and reflected waves. Greater water depth weakened shoaling and breaking and lowered the reflection coefficient overall; as the water depth increased from 0.481 to 0.556 m, the transmission coefficient rose from 0.243 to 0.780, the maximum rear-slope run-up from 0.069 to 0.214 m, and the reef-flat setup decreased, with secondary breaking observed under the deeper-water condition. These results reveal the redistribution of wave energy between the peak-frequency and low-frequency bands induced by the compound-slope topography, and the differentiated control of the incident conditions on wave setup and run-up, providing an experimental basis for their assessment in nearshore reef engineering.