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Abstract The development of a general‐purpose machine learning algorithm capable of quickly identifying optimal 3D‐printing settings can save manufacturing time and cost, reduce labor intensity, and improve the quality of 3D‐printed objects. Existing methods have limitations which focus on overall performance or one specific aspect of 3D‐printing quality. Here, for addressing the limitations, a multi‐objective Bayesian Optimization (BO) approach which uses a general‐purpose algorithm to optimize the black‐box functions is demonstrated and identifies the optimal input parameters of direct ink writing for 3D‐printing different presurgical organ models with intricate geometry. The BO approach enhances the 3D‐printing efficiency to achieve the best possible printed object quality while simultaneously addressing the inherent trade‐offs from the process of pursuing ideal outcomes relevant to requirements from practitioners. The BO approach also enables us to effectively explore 3D‐printing inputs inclusive of layer height, nozzle travel speed, and dispensing pressure, as well as visualize the trade‐offs between each set of 3D‐printing inputs in terms of the output objectives which consist of time, porosity, and geometry precisions through the Pareto front.