In the Langcang (Upper-Mekong) watershed, degraded watershed ecosystems in upland areas threaten cultivation practices, water resources, and dam development downstream. Assessment of ecosystem services and the factors that threaten them is an important first step to support watershed management. This, however, requires detailed information that is often missing in mountainous regions. To overcome this, in this paper, we adopt a decision tree approach to assess protection, biodiversity, and production services in two mountainous watersheds (Fengqing and Xiaojie) of the Lancang River Basin. Decision tree rules were built on the basis of field surveys, available references, ecosystem maps derived from remote sensing, expert knowledge, basic topographic information, and community interviews. Decision tree results showed that forest cover and agro-forestry practices contribute greatly to improved ecosystem functioning in the Fengqing Catchment compared to the Xiaojie Catchment. The results were consistent with field observations. The decision tree method proved to be a suitable and flexible tool for the rapid assessment of watershed ecosystem services, for highlighting those areas that need more in-depth research, and for guiding watershed and ecosystem management.