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[en] Small modular reactors (SMRs) are suitable for deployment in isolated underdeveloped areas to support highly localized microgrids. In order to achieve almost autonomous operation for reducing the cost of operating personnel, an autonomous control system with decision-making capability is needed. In this paper, a decision-making method based on Bayesian optimization algorithm (BOA) is proposed to explore the optimal operation scheme under fault conditions. BOA is used to adjust exploration strategy of operation scheme according to observations (operation schemes previously explored). To measure the feasibility of each operation scheme, an objective function that considers security and economy is established. BOA attempts to obtain the optimal operation scheme with maximum of the objective function in as few iterations as possible. To verify the proposed method, all main pump powered off fault is simulated by RELAP5 code. The optimal operation scheme of the fault is applied, the transient result shows that all key parameters are within safe limits and SMR is maintained at relatively high power, which means that BOA has the decision-making capability to get an optimal operation scheme on fault conditions.