The challenge presented by simultaneous buffer and service rate allocation in manufacturing systems represents a difficult non-deterministic polynomial problem. Previous studies solved this problem by iteratively utilizing a generative method and an evaluative method. However, it typically takes a long computation time for the evaluative method to achieve high evaluation accuracy, while the satisfactory solution quality realized by the generative method requires a certain number of iterations. In this study, a data-driven hybrid approach is developed by integrating a tabu search–non-dominated sorting genetic algorithm II with a whale optimization algorithm–gradient boosting regression tree to maximize the throughput and minimize the average buffer level of a manufacturing system subject to a total buffer capacity and total service rate. The former algorithm effectively searches for candidate simultaneous allocation solutions by integrating global and local search strategies. The prediction models built by the latter algorithm efficiently evaluate the candidate solutions. Numerical examples demonstrate the efficacy of the proposed approach. The proposed approach improves the solution efficiency of simultaneous allocation, contributing to dynamic production resource reconfiguration of manufacturing systems.