Political boundaries often do not coincide with ecological boundaries, and it is common for the same physical geographical unit to span multiple countries. Exploring establishing transboundary protected areas and ecological networks can effectively protect the integrity of natural ecosystems separated by political boundaries. Based on the integrated evaluation of ecosystem services function, ecological vulnerability, and ecosystem integrity, this study explored a methodological system for evaluating ecological protection priority areas in transboundary areas and selected the Altai Mountains, which span four countries, contain China, Kazakhstan, Russia, and Mongolia, as a typical case to conduct empirical research. The study found that the extremely important areas of ecosystem services function, ecological vulnerability, and ecosystem integrity showed transboundary contiguous characteristics. Furthermore, weighted overlay analysis identified the spatial distribution pattern of ecological protection priority areas in the Altai Mountains. We suggested establishing transboundary protected areas in the four countries’ transboundary areas, building the identified ecological protection priority areas and existing protected areas into a transboundary protected area network, and deepening a multi-party transboundary protection cooperation mechanism. This study can provide a theoretical and practical reference to achieve the 2030 biodiversity conservation goals.