The modal frequencies of super high-rise buildings in high winds may exhibit time-varying characteristics, which affect the control performance of tuned liquid dampers (TLDs). This paper proposes an optimal design method for MTLDs considering structural frequency uncertainty, with TLD plane size, liquid depth and damping screen density ratio as design variables and frequency-dependent comfort based on AIJ2004 as constraints. The structural frequency uncertainty is used as a constraint to calculate the response of the controlled structure using an equivalent linear model, and an iterative method is used to consider the effect of the damping amplitude-related characteristics of the damping screen to improve the accuracy of the calculations, and the MTLD scheme is obtained by the particle swarm algorithm with the optimisation objective of the minimum total water volume. The method is applied to the optimal design of the MTLD for a 310 m high super-tall building and the results are compared with those of two other non-optimised single TLDs and MTLDs. The results show that the method is robust and the optimised solution meets the comfort performance level within 10% frequency variability and reduces the total water volume by 13.2% compared to the conventional TLD. Finally, the effectiveness of the optimised scheme is verified using the structure-MTLD nonlinear multimodal model.