Housing structure is a principal factor of seismic vulnerability in Chinese rural areas. Therefore, analyses on the economic, geographic and cultural factors underlying the spatial differentiation of housing structures are very important for assessing the vulnerability of different regions. In this paper, a database of rural housing structures of 2699 counties all over China was established based on the Fifth National Census in 2000, where housing structures were divided into three types by the materials of bearing structures, i.e., reinforced concrete, brick-mixed and traditional (including houses made up of wood, grass, bamboo or other materials that are not standard). Then, the spatial patterns of rural housing structures were examined at both regional and county scales. It was found that, brick-mixed structure was the most important housing structure type in rural China, and the proportion of traditional housing structure was very high in the western region (close to 50%). Further analysis revealed that the distributions of traditional and brick-mixed structure houses were significantly influenced by the climate, rural economy and culture. The increase of incomes of rural citizens would prompt the shift of rural houses construction from traditional houses to brick-mixed ones. The proportion of the reinforced concrete structure houses in rural areas was generally low, but higher in the eastern and central regions than in the western region. Factors affecting the distribution of reinforced concrete structure houses include the climate, non-agricultural employment and township economy. It is suggested that the primary purpose of rural policies should aim to increase farmers’income to lower the degree of the seismic vulnerability in rural areas. Besides that, promoting the concentration of population in towns instead of in rural areas and gradually disseminating and applying the anti-seismic standards of house-building are also needed.