This paper presents a robust optimal design method for a periodic structure type of MEMS resonator that is vulnerable to mode localization. The robust configuration of such a MEMS resonator to fabrication error is implemented by changing the regularity of periodic structure. For the mathematical convenience, the MEMS resonator is first modeled as a multi-pendulum system. The index representing the measure of mode variation is then introduced using the perturbation method and the concept of modal assurance criterion. Finally, the optimal intentional mistuning, minimizing the expectation of the irregularity measure for each substructure, is determined for the normal distributed fabrication error and its robustness in the design of MEMS resonator to the fabrication error is demonstrated with numerical examples.