Natural heritage sites are common wealth of mankind. The protection and restoration of such sites must not be neglected in the process of reconstruction after the 5.12 Wenchuan Earthquake in Sichuan Province, China. Taking Dujiangyan city as a case study, this paper discusses the issues of protection and restoration of natural heritage sites. First, the authors, through field investigation, find out the damages to the natural heritage sites in Dujiangyan caused by the devastating earthquake. We then analyze the spatial patterns of geological hazards and ecological fragility of the Dujiangyan region. Based on the study results and the varying characteristics of different natural heritage sites, a planning framework and some feasible measures for post-earthquake reconstruction are suggested.