This study takes the three industries and the internal structure of tertiary industry in ecological conservation development area of Beijing from 2005 to 2012 as the research object, using shift-share analysis method, comprehensively analyses of the development of industry share deviates from the components, structure deviation and competitiveness deviation component, provides some reference for choosing the leading industry in ecological conservation development area and the adjustment of industrial structure. The results shows that the first industry in ecological conservation development area has a certain but small amount competitiveness, cannot effectively promote economic development of the whole area; the second industry growth in ecological conservation development area is slower than the average level in Beijing, and does not have the competitive advantage; the total deviation vector of the third industry presents the obvious rise, and accelerates the development trend, which is the main force of the regional economic development in the future. In potential leading industry selection for districts and counties, Mentougou District takes the culture, sports and entertainment industry, and finance industry as leading industries, Huairou District takes the information transmission, computer services and software industry as the leading industry, Pinggu District takes the culture, sports and entertainment industry as leading industry, in the present stage of the third industry in Miyun County has not meet the requirements of the industry, and the estate industry is the leading industry for Yanqing County. Comprehensive tourism is suitable for the dominant industry of ecological conservation development area, and is also in line with the industry development present situation and future development direction. That can effectively promote regional economic development.