Synthetical eco-environmental problems’ treatment is a new stage for certain pollutant control or ecological restoration. Traditional urban planners have focused more on social–economic development but less on eco-environmental considerations. Spatial planning is currently an essential administrative management method for regional development and eco-environmental protection in China. National and provincial spatial planning designs general strategies, and prefecture-level planning is the most important scale for spatial management. For scientific, spatial governance for eco-environmental protection, we propose a synthetic spatial analysis and planning method framework that involves atmospheric, edaphic, hydrographic, and ecological processes to identify pivotal regions for regional eco-environmental security goals. The synthetic method was conducted using advanced models including the CMAQ and SWAT models and spatial statistical methods. A Chinese prefecture-level city, Anshan City, was chosen to fulfill the method framework due to its various ecosystem types and environmental problems. A total of 67 eco-environmental management units (EMU) were divided based on atmospheric pollution patterns, hydrographic processes, edaphic heavy metal pollution, and ecological spatial analysis. Each unit was identified with ecological or environmental risk and a proposed management regulation. For considering the whole eco-environmental process, the ecological security pattern (ESP) was constructed. The results showed that 166 corridors were identified with an area of 2241.25 km², with enhanced connectivity among 76 ecological sources (12.27% of Anshan City). By coupling two results, the optimized ecological conservation and restoration pattern was proposed, in which priority protection areas were identified. This synthetic method can provide scientific analysis and guidance to support spatial planning and ecological construction for multi-purpose ecological and environmental protection.