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The intensification of global climate change has led to a widespread consensus on carbon reduction, with the power industry being the principal contributor to carbon emissions necessitating an inevitable transition of its energy structure. Concomitantly, the escalating frequency of natural disasters caused by extreme weather presents formidable challenges to both secure power supply and the low-carbon transition of the power system. To fulfill the developmental requirements of a low-carbon power system and address the carbon emission risks imposed by natural disasters, this paper proposes a bi-level model for generation expansion planning (GEP) that incorporates constraints on the carbon emission trajectory and the influence of natural disasters. The planning-level model optimizes investment costs of various generation technologies and energy storage (ES), as well as the overall operational expenses over the planning period, with an objective to minimize them. It incorporates carbon emission trajectory constraints and policy constraints, such as carbon peaking, carbon neutrality and renewable energy (RE) penetration rates, in order to optimize the planning installed capacity of power sources. The operational-level model aims to minimize typical daily operating costs while also simulating power unit outputs in routine and disaster scenarios. A case study is conducted in a disaster-prone province in southern China to analyze the power generation expansion planning and the trajectory of carbon emissions from 2020 to 2060 under different scenarios. The simulation results show that compared to thermal power, the planning scheme mainly focused on RE with ES is better suited to achieve the goal of a low-carbon transition of the power grid. Moreover, after considering natural disasters, the cost and carbon emissions of power system planning are higher, and the risk of carbon emissions increases with the severity of disasters. • A multi-time scale bi-level low-carbon GEP model is proposed. • Natural disaster scenarios and low-carbon policy constraints are considered in the GEP model. • Carbon emission trajectory of the planned power system is estimated and introduced as a constraint into the GEP model. • Evaluation indicators that comprehensively consider low-carbon performance and economic feasibility are proposed. [ABSTRACT FROM AUTHOR]