In the context of ecological civilization construction, China is gradually building a system of nature conservation areas with national parks as the mainstay to implement the need for the protection and management of natural resources and cultural heritage. For the various types of nature parks in the present situation, it is urgent to assess their values and propose methods to resolve each control line’s contradictions, comprehensively delineate the zoning areas and adequately protect them in response to the zoning areas. At the conceptual level, the similarities and differences between the functional classification, control zones, management agencies, and implementation methods of various control lines, as well as the relationship between the “three zones and three lines” of territorial spatial planning and the control lines of nature reserves, are sorted out and analyzed. In the specific planning and management, the contradictions and conflicts of various control lines are coordinated through the security pattern approach. The coordination method of “intersection, integration, and complementation” is used to delineate four control lines: strictly protected areas, ecological conservation areas, traditional use areas, and scientific and educational recreation areas, and formulate zoning control plans. Taking Leiqiong World Geopark Haikou Park as an example, we construct a geological disaster security pattern, heritage security pattern, biodiversity conservation security pattern, hydrological security pattern, and recreation security pattern and establish a comprehensive security pattern by the overlay. With the method mentioned above, we coordinate existing natural protected area partition, national geological relics reserve, ecological protection red line, identification of mandatory protection and resilient use, and put forward relevant strategies.