The concentrations of five metals (Cu, Pb, Zn, Cd and Hg) were measured in sediments obtained before and after the establishment of Techeng Island Special Marine Reserves (TCISMR) in Zhanjiang Bay to evaluate the ecological risk of heavy metals. The results showed that average values of potential ecological risk indexes of heavy metals at all stations increased slightly from 32.09 to 30.54 after establishment of TCISMR. Optimal semivariance simulation showed that the contents of five heavy metals have strong spatial correlations in August 2010 (before), while this correlations weakened in April 2013 (after establishment of TCISMR), suggesting that the main sources of heavy metals changed. The Hakanson Risk Index (HRI) values in Donghai levee, central and southern parts of Zhanjiang harbor were high up to 60.13 and 46.46, respectively. And Zhanjiang Bay Channel, the areas around special marine reserves, the artificial reef areas and mangrove areas at south of Techeng Island are the areas with low ecological risk and high ecological value, which should be treated as the prior ecological protection areas. Our study provided a priority control pattern of heavy metal pollution in TCISMR, which greatly benefits the sustainable development and resource protection in Zhanjiang Bay.