Developing methods for measuring multi-dimensional poverty and improving the accuracy of poverty identification have been the hot topics in international poverty research for decades. In light of the academic thoughts of the vulnerability and sustainable livelihood analysis framework, this paper establishes an index system and a method for geographical identification of multi-dimensional poverty, and carries out a county-level identification in rural China. Furthermore, this study makes a comparison between the identification result, income poverty and the latest designated poor regions by the Chinese government. At last, the identified multi-dimensional poor counties are classified by the similarity of poverty reduction measures. The results show that: (1) Taking the vulnerability and sustainable livelihood analysis framework proposed by DFID as theoretical basis, we build an index system of multi-dimensional poverty identification to reflect the farmers' livelihoods that multiple factors work on. It is feasible to develop a composite Multi-dimensional Development Index (MDI) for the integrated method of geographical identification of multi-dimensional poverty in rural China. (2) A total of 655 counties are identified as multi-dimensional poor counties. They are concentrated and jointly distributed in space, in which the Tibetan Plateau and its neighboring areas of three prefectures in southern Xinjiang, western Loess Plateau, mountainous and gully areas in western Yunnan and Sichuan, are suffering greatly from poverty. Besides, poor counties are mainly in Wumeng-Daliang mountainous areas, Yunnan-Guizhou-Guangxi rocky desertification areas, border mountainous areas in Yunnan, Wuling mountainous areas, Qinling-Daba mountainous areas, Shanxi-Shaanxi gully areas and Yanshan-Taihang mountainous areas. (3) In comparison to the latest designated poor counties, this paper targets at poor counties with more disadvantages at both single and multiple dimensions. Some 71.79% of designated poor counties overlap with identified poor counties. By contrast, the majority of the designated poor counties located in mountainous areas of central or eastern China do not belong to identified poor counties because of much less disadvantage/deprivation dimensions. However, the identified poor counties, which are mainly distributed in marginal areas of plateau or mountainous areas in western China, and suffering from multiple dimensions of disadvantages and deprivations, are not included in the designated poor counties. (4) According to the disadvantage/deprivation situation of different dimensions, multi-dimensional poor counties are classified into eight types, i.e., lack of financial capital, lack of human capital, lack of infrastructure, lack of both financial capital and infrastructure, lack of both human capital and infrastructure, lack of means/strategies of livelihoods, lack of living condition, and lack of development condition.