Indian Himalayan Region (IHR) is prone to climate shock and is highly sensitive to minor climate variance. Yet, there is a dearth of studies evaluating the adaptive capacity and vulnerability of the socio-ecological system. We assessed the household (n = 1346) and village (n = 77) level adaptive capacity and vulnerability to climate stress in Beas, Bhagirathi, and Teesta basins of IHR following a bottom-up approach. The estimation of adaptive capacity scores for surveyed households and villages were done based on preselected indicator scores of the natural, human, financial, and physical capital assets. The exposure to climate shock was obtained from Coupled Model Intercomparison Project (CMIP5) data of different scenarios. The present and future vulnerability scores were assessed based on the adaptive capacity, exposure and sensitivity to climatic shock. The villages and households were grouped in resilient and vulnerable clusters, and major indicators determining the vulnerability were identified. Our result revealed the household and village level adaptive capacity were low in the Bhagirathi and Teesta basin compared to the Beas basin, so as the present and future climate shock. We found that access to different resources as well as natural and financial capital assets were the major governing factor for the adaptive capacity of the villages. We suggest future policy interventions to be on climate sensitive sectors, mostly the natural capital of the region as part of the adaptation and mitigation strategy to climate change.