The dry valleys of Southwest China specifically refer to a type of azonal landscape distributed in the large river basins of the Hengduan Mountain ranges, and are the outcome of the effects of the monsoon climate, ridge-valley geomorphology, and long-term human perturbations. The dry valley landscape is characterized by prominent seasonal aridity, a vertical climate gradient, rich flora of high endemism, and unique vegetation types well adapted to the distinct environment. The environmental change in the last decades is characterized by consistent climate warming and widespread anthropogenic disturbances, especially land use/land cover changes mainly driven by road building, hydro-power construction, mining, and urbanization. These human disturbances intensified vegetation fragmentation, soil erosion, habitat degradation and biological invasion. Environmental degradation has threatened biodiversity resources and ecosystem security while the conservation measures for this unique ecosystem are lacking. We appeal for attention and timely action of biodiversity conservation in the dry valleys of Southwest China by means of establishing natural reserves. Meanwhile, contingent planning for vertical agriculture, degraded vegetation restoration, utilization program for the unique species resource and ecotourism are critical maintaining the sustainability of the dry valley ecosystems. Moreover, the policy and strategy under the goal of ecological civilization construction are also important tools to be applied in promoting ecosystem services and ecological security in the dry valleys of Southwest China.