Optimization design was widely used in the high-lift device design process, and the aeroacoustic reduction characteristic is an important objective of the optimization. The aerodynamic and aeroacoustic study on the baseline wing and flap configuration was performed numerically. In the current study, the three-dimensional Large Eddy Simulation (LES) equations coupled with dynamic Smagorinsky subgrid model and Ffowcs–William and Hawkings (FW–H) equation are employed to simulate the flow fields and carry out acoustic analogy. The numerical results show reasonable agreement with the experimental data. Further, the particle swarm optimization algorithm coupled with the Kriging surrogate model was employed to determine optimum location of the flap deposition. The Latin hypercube method is used for the generation of initial samples for optimization. In addition, the relationship between the design variables and the objective functions are obtained using the optimization sample points. The optimized maximum overall sound pressure level (OASPL) of far-field noise decreases by 3.99 dB with a loss of lift-drag ratio (L/D) of less than 1%. Meanwhile, the optimized performances are in good and reasonable agreement with the numerical predictions. The findings provide suggestions for the low-noise and high-lift configuration design and application in high-lift devices.