The study of transboundary territories is an urgent and complex issue of geography since currently there is no well-developed methodology for studying these objects and there are only sectoral approaches to those. The landscape-ecological analysis of transboundary territories with their own characteristic set of relationships between man and nature should be based on a systematic approach that allows the geographical objects with different intersystem connections to be studied. From the point of view of system approach, the object of the study is a set of transboundary systems. In addition, the study of transboundary territories is possible due to the complexity of the study which is based on the landscape theory, the doctrine about geo-systems by B. V. Sochava and the system of geo-ecological research methods. The paper presents current trends of the study of transboundary objects and processes, throws light upon some basic approaches to the study of transboundary geo-systems and defines three types of transboundary geo-systems. The main theoretical and methodological propositions of geo-system analysis are outlined. The problems of landscape-ecological analysis of transboundary geo-systems are considered on the example of the Selenga River Basin. The stages of the study, including geo-systematic and geo-ecological analysis, socio-economic study of the territory and an assessment of the landscape-ecological situation are proposed. Taking into account complexity and variety of aspects of transboundary territories, multi-aspect studies are pointed out that reveal both genesis of natural complexes and geosystems sustainability, socio-economic factors that effect exploitation and transformation of natural objects and the formation of different landscape-ecological situations.