[Purposes] An investigation of the influences of reef crest on the wave height of irregular waves and wave setup over the reef flat is reported in this pape. [Methods] A non-hydrostatic numerical wave model was used to simulate a series of test cases under different still water depths over the reef flat, wave heights, and wave periods, and to compare the difference of wave evolution process in the presence and absence of a reef crest. [Findings] Results showed that, the depth reduction under the presence of reef crest caused significant enhancement to the wave breaking tensity at the reef edge while shortening the width of the surf zone; the reef crest caused a decrease in the wave height and an increase in the wave-induced setup at the reef end; the effects of the presence of a reef crest to the wave height and wave-induced setup at the reef end first increase and reaches a maximum with increasing reef flat water depth, before begin to decrease; with the presence of reef crest, the wave height and setup at the end of the reef increased with incident wave height and spectral period.[Conclusions] The reef crest influences the wave height and setup at the end of the reef flat by altering the wave-breaking process near the reef edge, and the degree of influence is closely related to the still water depth (tide level) of the reef crest; the results of this paper can provide a reference for coral reef coastal disaster prevention and mitigation.