Trans-boundary aquifer is an aquifer system that exists in more than one state. The paper analyzes hydrogeological conditions of Lancang-Mekong River Basin and delimits trans-boundary aquifer systems, as well as explores the groundwater resources and environmental problems. The paper puts forward trans-boundary aquifers comprehensive evaluation index system, and applies it to the four trans-boundary aquifers in the Lancang-Mekong Basin. The study is of significance for the management of Lancang-Mekong River trans-boundary aquifers and the construction of harmonious international environment in Southeast Asia.