Rapid population growth and increased economic activity impose an urgent challenge on the sustainability of water resources in Beijing. Water resources system is a complex uncertain system under climate change which is of vulnerability. But water resources system vulnerability research is relatively weak. In this study, we present a multifunctional hierarchy indicator system for the performance evaluation of water resources vulnerability (WRV) under climate change. We established an evaluation model, i.e., analytic hierarchy process combining set pair analysis (AHPSPA) model, for assessing WRV, in which weight is determined by the analytic hierarchy process (AHP) method and the evaluation degrees are determined by the set pair analysis (SPA) theory. According to the principle of scientificalness, representative, completeness and operability, the index systems and standard of water resources vulnerability evaluation are established based on the analysis of sensibility and adaptability which include five subsystems: climate change, water resources change, social and economic infrastructure, water use level and water security capability. The AHPSPA model is used to assess water resource vulnerability in Beijing with 26 indexes under eight kinds of future climate change scenarios. Certain and uncertain information quantity of the WRV is calculated by connection numbers in the AHPSPA model. Results show that the WRV of Beijing is in the middle vulnerability (3 or III) under above-mentioned different climate change scenarios. The uncertain information is between 37.77 and 39.99 % in the WRV evaluation system in Beijing. Compared with present situation, the WRV will become better under scenario I and III and will become worse under scenario II, scenario IV, scenario representative concentration pathways (RCP)2.6, scenario RCP4.5, scenario RCP6.0 and scenario RCP8.5. In addition, we find that water resources change and water use level factors play more important role in the evaluation system of water resource vulnerability in Beijing. Finally, we make some suggestions for water resources management of Beijing.