The weakening Indian monsoon during recent warmer decades has caused greening and browning trends in water- and energy-limited terrestrial ecosystems of the Tibetan Plateau, respectively. Little is known, however, on the underlying mechanisms of such divergent responses of vegetation to the monsoon weakening. Herein, using the Indian monsoon index, high-resolution vegetation indices and multi-source climate data, we assessed the response of vegetation greenness to the Indian monsoon from 2000 to 2018 in two adjacent basins dominated by water- and energy-limited ecosystems and located in the southeastern Tibetan Plateau. The two basins showed opposite greenness trends due to direct and indirect effects of the weakening monsoon. The weakening monsoon increased vegetation greenness in the humid sites due to more heat exposure and solar radiation, but not in dry sites because of amplified drought stress. Thus, a weaker monsoon would not favor productivity in drought-prone ecosystems, whereas it would benefit energy-limited sites due to more radiation and warmer conditions associated to lower cloudiness. The effect of atmospheric circulation and its inter-decadal oscillation on basin-scale ecological processes should be therefore taken into account to refine earth system models and climate forecasts.