The optimal design of multiple tuned liquid dampers (MTLDs) is important for improving structural vibration control. However, current MTLD optimization studies typically take the response of the original structural frequency as the optimization objective, without considering the effect of the structural frequency shift under strong wind loads. Therefore, this paper proposes an MTLD frequency optimization method based on the weighted average of structural acceleration magnification factors. This method can target multiple responses in the structural frequency shift region, thereby overcoming the limitation that the optimal parameters can only be solved for a single structural frequency. It is also worth noting that this method can be applied to the frequency optimization of MTLDs with internal obstructions. A detailed procedure for determining the optimal frequency distribution of the MTLD based on a particle swarm algorithm is presented, and a coupled simulation method for the vibration response of the structure-MTLD system is developed to demonstrate the validity of the optimization results. The proposed optimization method is then further applied to the design of the MTLD with paddles for wind-induced vibration control in a 206 m super high-rise building. The results demonstrate that the modified MTLD optimization, which considers multiple structural frequencies, exhibits superior robustness compared to the traditional MTLD optimization, which considers only one original structural frequency. This implies that the modified MTLD can effectively mitigate the detuning effect caused by the structural frequency shift, which is beneficial for the practical design and application of the MTLD.