Abstract: Guizhou is one of the provinces with the most widely distributed carbonate rocks and extensive karst systems. The area under karst is 120 000 km², and ≈1/3 of the area is rocky desert. About 5.85 million people of the rural population are poor, which is a growing concern for fast-developing country. Using eco-economy and systematic coupling theories, this paper developed an evaluation index system for Qianxinan Region, Guizhou Province. About 15 years of data, spanning for 1994~2009, were used in the study. Modeling was used to explain the interactions/coupling mechanisms of compound rural-urban eco-economic system in karst regions which was in turn used to develop a material foundation/dynamic mechanism. The results suggested that preface parameters in the compound urban-rural eco-economic systems of Qianxinan Region were growing. This was mainly due to rapid growth of the urban eco-economic system. While the positions of rural and urban economies changed in the compound system, urban economy showed a great momentum with a gradually strengthened dynamic human input. Environmental elements were damaged to some degree, especially in rural area environmental factors changed greatly. The coupling function was used to calculate the coupling degree (DC) and coupling coordination (CC) of the compound urban-rural eco-economic system in karst areas. The calculation showed that DC of the compound urban-rural eco-economic system was 0.39~0.49 with a CC of 0.18~0.42, they were considered not high, but with gradual built up of subsystems synergy. DC of the rural eco-economic system in karst areas was 0.48~0.50 with CC of 0.18~0.29, it suggested non-adaptation of ecological environment to rural economic development. DC of the urban eco-economic system in karst areas was 0.15~0.50 with CC of 0.05~0.33, they was not high, but indicted a rapid phase of development. This brought about negative influences on the environment. Based on the present conditions of the compound system, it was advanced that rural eco-economic system growth should promote urban eco-economic construction, to realize healthy development of the compound system.