When using meta-heuristic optimization approaches for optimization, a large number of samples are required. In particular, when generating a subgeneration, the utilization of existing samples is low and the number of individuals is high. Therefore, surrogate-based optimization has been developed, which greatly reduces the number of individuals in the subgeneration and the cost of optimization. In complex air supply scenarios, single-objective optimization results may not be comprehensive; therefore, this paper developed a double-objective air supply optimization method based on the Kriging surrogate model and Non-dominated Sorting Genetic Algorithms-II. And it proposed the infill criteria based on clustering to advance the Pareto Frontier. The method was validated with an inverse prediction case, and in particular, the problems when based on 3D steady-state simulations were analyzed. The results showed that the method can quickly achieve an approximate prediction of the boundary conditions (when predictions were made based on experimental data, the number of simulations was 82 and the average error was 6.8%). Finally, the method was used to optimize the air supply parameters of a dual-aisle, single-row cabin, with only 118 samples used in the optimization process. The Pareto set suggested that an airflow organization with dual circulation may be optimal.