In this article, Reef Check (coral reef health survey procedure) and factor analysis of coral reef ecosystem health index were used to evaluate the health status of the coral reefs at three sites (Zhuzheliao, Gongshan and Niubeikeng) of the Weizhou Island, Beihai, Guangxi Province from 2001 to 2012, focusing on fishes, invertebrates and reef substrates. The investigation results indicated that, during the nine years, coral reef ecological conditions showed big differences in different peripheral regions of the Weizhou Island. Although coral reef coverage was stable in Zhuzheliao and Niubeikeng, dominant population changed. But in Gongshan, coral death has occurred over a large area since 2002 and has not recovered up till now. Invertebrates were at extremely low levels, and fishes were also poor in both population quantity and diversity. This indicated that in this region, the coral reef ecosystem bore a heavy pressure from human activities.