A significant number of protection gaps in nature reserves are present in China, hindering the overall development of the nature reserve system. Most analyses of these protection gaps are grounded in evaluating ecosystem service functions; however, only some studies have quantified ecological sensitivity, making it challenging to fulfill current analysis requirements. The assessment of ecosystem service functions’ importance and ecological sensitivity serves as a crucial means for determining ecological protection spaces in China. Using Weihai City as a case study, this article identifies the ecological spaces and protection gaps in nature reserves based on evaluating ecosystem service function importance and ecological sensitivity while providing optimization suggestions. Research results show that Weihai City has significant ecological resource advantages, and the areas with medium and above ecological evaluation are mainly distributed around nature reserves and some mountainous regions; the proportion of ecological space in nature reserves is 66.3%, with a relatively low proportion in wetland parks and natural protected areas; there are 497.4 km2 of ecological space outside nature reserves that have not been protected, and the gap areas show a distribution pattern of small aggregation and large dispersion. In the future construction and integration optimization of nature reserves, ecological restoration and zoning management should be carried out in wetland parks; unsuitable natural protected areas should be downgraded or revoked; and external protection gaps should be classified and incorporated into the nature reserve system in stages.