Abstract: Soil and water resources are vital basic resources in mankind’s living and development progress. The Loss of soil and water resources caused by soil erosion has already seriously obstructed economy development of our country, which has been the first environmental problem. Therefore, it is essential for our country to carry out comprehensive management of soil erosion, with small watershed as unit. After 50 years of exploration and development, the achievements of the small watershed management model are positive and remarkable. However, many weaknesses and outstanding theoretical problems we faced must be resolved. In order to solve the outstanding theory problems and provide some references for future study, this paper summarized the problems existed in comprehensive management of small watershed from the following aspects: soil erosion, hydrology and water resources, ecosystem economy, health, environment and ecosystem engineering.