Along with rapid economic growth and urban sprawl in China, biological conservation and biodiversity loss in and around cities has become an increasingly important topic for discussion, especially in rapidly urbanizing regions. One of the most urgent threats faced by growing cities is habitat loss, degradation and fragmentation. Focused on this threat, this paper distinguishes the significant habitats and spatial patterns that are of vital importance to biological process and conservation at the landscape scale using Lambeck′s (1997) Focal Species Approach which selects the most sensitive species to a certain threat, whose requirements are believed to encapsulate the needs of other species. The paper also applies Yu′s (1996) Security Pattern Theory which identifies landscape areas and elements of critical significance in safeguarding the process of species maintenance and dispersal. Beijing is an ideal region for employing these approaches and theories because of its: high percentage of urbanized land (84.9% in 2008); corresponding loss and fragmentation of habitats, rapid population increase; and abundant bird species. According to the definition of focal species and a set of specific criteria, Large egret (Casmerodius albus), mallard (Anas platyrhynchos), and ring-necked pheasant (Phasianus colchicus) were chosen as focal species for Beijing among hundreds of candidate species, mainly because of their varied biological characteristics, and the threatened typical habitat types they represent, which are assumed to represent most of the habitats in the whole region. With the aid of a geographic information system (GIS) spatial analysis model, security patterns for individual species were defined as follows: Step 1: a vertical habitat suitability analysis in which the optimum areas for species were selected as the movement sources, and Step 2: a movement resistance surface analysis, which was executed by simulating the horizontal movement across the landscape of the species, through the Minimum Cumulative Resistance (MCR) model. These three individual patterns were considered of equal importance, and were overlaid into a comprehensive biological conservation security pattern with three different security levels to “defend” different conservation situations. A comprehensive biological conservation security pattern plan and relative conservation strategies for Beijing were proposed, including the conservation cores, buffer zones, inter-source linkages and strategic points. This plan is based on the spatial character of the calculated resistance surfaces and general principles in biological conservation. The result showed that, the security pattern plan has a significant decrease in Patch Number (-45.05%), Landscape Division Index (-82.71%) and Mean Euclidean Nearest Neighbor Distance Distribution (-14.51%), as well as a significant increase in Mean Patch Area (85.36%) and Largest Patch Index (45.40%), with only 1.03% increase in total area, which finds that the plan can protect core habitats and critical spatial patterns in Beijing by covering about 60% of the total land. This research concludes that the Security Plan can effectively relieve habitat loss, degradation and fragmentation, and thus support the goal of protecting biodiversity in the whole region. The methods and results, which possess both theoretical and practical value, could provide a defensible decision-making basis for biodiversity conservation and ecological construction in Beijing, as well as for similar research in rapidly urbanizing areas.