Due to the inference of the uneven shallow water seabed and the surrounding islands, the wind-generated waves around or in a reef lagoon are rather complicated, and critical to the safety of floating structures deployed near islands or inside a lagoon. This paper aims to find a feasible analysis tool for the wave simulations near islands and reefs. The proposed three methods of grid techniques of WAVEWATCH III (WW3) are assessed by using on-site measured data which was collected and accumulated for about 5 years since August 2014 by a wave observation system deployed inside and outside a reef lagoon in South China Sea. In the assessments, the wave statistics including the correlation coefficients, root mean square errors, and their variances are used to quantify the precisions of the simulation results of the significant wave heights, mean wave periods, and peak wave directions at two sites. Among the three methods, the Multi-scale Zone and Multi-scale grid Technique (MZMGT) established on unstructured triangular grids exhibits better results in terms of the accuracy and CPU cost. In addition, the bimodal feature of wave spectra was observed at both sites of the reef lagoon in different typhoon events. The wave characteristics inside the reef lagoon and open sea are also analyzed.