Abstract: Heat pipe reactor has the advantages of miniaturization, high inherent safety, and simple structure, which has extensive application prospects and research significance in the fields of universe exploration and distributed power generation. A megawatt heat pipe reactor is typically required to arrange thousands of heat pipes in a limited space to export the heat from the core, which increases system complexity and impedes engineering technology realization. To solve this problem, a novel design was proposed in this paper in which the flat heat pipe arrays and plate type fuel elements were tightly fitted to form an integrated core, which has the characteristics of compact structure, small and invariable thermal contact resistance, and stable operation under various operating conditions. Non-uniform heating is common in the actual heat transfer process of the core. The flat heat pipe should be able to achieve stable operation under the non-uniform heating condition to cool the core. Thus relevant research is necessary to clarify the influence of non-uniform heating on the flow and heat transfer characteristics inside the flat heat pipe and verify the feasibility of the flat heat pipe for core cooling. Based on this background, the three-dimensional thermal-flow-solid coupling analysis model of the minimum feature unit of the flat heat pipe array was established using COMSOL multiphysics software, and the research on the thermal-hydraulic and mechanical characteristics of the flat heat pipe under non-uniform heating conditions was conducted in this paper. The reliability of the numerical model was validated by comparing it with the literature. The relative deviation between the numerical simulation result and the experimental reference value is less than 5%. The rationality of a composite wick structure with special type arteries was analyzed using the above numerical models. The results show that the wick structure effectively reduces the flow resistance by changing the liquid return path, making the flat heat pipe work stably. The heat transfer and flow characteristics inside the flat heat pipe under various degrees of heating unevenness were studied, where the symbol Uf was used to define the degree of unevenness in this work. It was found through qualitative research and quantitative analysis that the temperature distribution on the wall surface of the evaporator of the flat heat pipe is affected by the non-uniform heating conditions, and the heat transfer and flow characteristics of the flat heat pipe are not, which suggests that the flat heat pipe could maintain good heat transfer performance and temperature uniformity. The thermal stress distribution of the flat heat pipe under different degrees of heating unevenness was studied furtherly. The results show that non-uniform heating increases the thermal stress of the shell of the flat heat pipe, the peak stress is on the vertex of the front end of the flat heat pipe; this does not cause material failure, and the working stress of the flat heat pipe is within the creep limit of the structural material at high operating temperature. Results of this study show the ability to realize the performance assessment of the flat heat pipe under non-uniform heating conditions, verify that the flat heat pipe designed in this paper could meet the demand of core cooling, and provide a reference method for the performance analysis of related untraditional heat pipes under special conditions.