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[Display omitted] • A bi-level joint-probabilistic programming approach is developed. • It can handle leader–follower issues and joint-probabilistic constraints. • The proposed approach is applied to China's multi-regional energy system model. • The optimal schemes during 2021–2050 under three mitigation scenarios are obtained. • Results are helpful to achieve low-carbon goals in multi-regional energy system. Climate change mitigation and renewable resources utilization are becoming particularly urgent for energy system management. In this study, a bi-level joint-probabilistic programming (BJPP) method is developed for planning multi-regional energy system under different mitigation policies and uncertainties. BJPP can handle leader–follower issues in decision-making process as well as examine the risk of violating joint-probabilistic constraints. Based on the BJPP method, a China's multi-regional energy system (named as BJPP_CMES) model is formulated to provide optimal scheme for energy system planning of China over a long-term horizon (2021–2050) by synergistically minimizing carbon dioxide (CO 2) emission and system cost. A series of scenarios associated with different carbon capture and storage (CCS) levels and violation risks of energy-demand constraints are examined. Results reveal that: (i) the share of non-fossil energy in China's energy supply would keep increasing in 2021–2050, and the highest growth of the renewable supply would occur in Ningxia (rising 47.7%); (ii) Sichuan, Inner Mongolia, and Gansu would be the top three suppliers of renewable electricity; (iii) the CO 2 emission of China would reach a peak of [44.3, 54.8] billion tonnes during the period of 2026–2030; Shandong, Inner Mongolia, and Shanxi would be main contributors of CO 2 emission in the future; (iv) compared with the single-level model, the CO 2 emission from the BJPP_CMES model would reduce by [2.7, 5.7]%; (v) among developed regions, the individual probability level of Jiangsu-Zhejiang-Shanghai is the most significant parameter for both CO 2 emission and system cost. The findings are helpful for decision makers to optimize multi-regional energy system (MES) with a low-carbon and cost-effective manner, as well as to provide useful information for renewable energy utilization and regional sustainable development. [ABSTRACT FROM AUTHOR]