An innovative open natural circulation system is proposed in this work, which utilizes the difference of the heat flux loaded on different parts of the pipe to form a self-circulation flow of working fluid. Via CFD simulation established by embedding self-programmed code into commercial software, the transient performance of a three-dimensional natural circulation loop is studied. The results indicate that: applying uniform heat flux on the wall of the loop, the fluid flow state successively experiences three stages, i.e., liquid expansion, partial circulation, and phase change, and finally a vapor plunger blocks the pipe, leading to local heat transfer deterioration and temperature increase; applying non-uniform heat flux, the fluid can be driven to form self-circulation flow, which can not only cool the structure via convection, but also prevent bubbles from accumulating, stabilizing the maximum temperature of the system around the boiling point; further for the loop with a more complex configuration, the self-circulation can be also started but with different start modes. Therefore, the new natural circulation system can achieve effective and adaptive cooling according to the external thermal environment, avoid fluctuation and vapor block phenomenon caused by violent phase change, and reduce the driving equipment and control unit. This work provides a reference for the design of the natural circulation system applied in a non-uniform heating environment. Through transient numerical simulation of the start-up stage, the fluid flow, phase change, and heat transfer characteristics in the natural circulation loop are studied, and the start mode and mechanism are analyzed.