Multiple variable frequency pendulum isolator (MVFPI) has been recently developed as a superior alternative to the traditional friction pendulum bearing (FPB) especially for the seismic isolation in near-fault regions. The MVFPI is characterized by its variable frequency and self-adaptability, which are achieved by piecewise function of sliding surface and shape memory alloy (SMA). The objective of this study is to propose the design algorithm of the MVFPIs in highway bridge as an extension of the direct displacement-based design (DDBD) framework. The nonlinearities of the structural components are taken into account in the design procedure, and the corresponding damage states satisfy the two-stage design philosophy. The accuracy and robustness of the design procedure are verified by an isolated four-span highway bridge through nonlinear time history (NLTH) analyses. The analytical results indicate that the proposed design procedure can predict the profile of deck displacement and amplitude, as well as the damage states of the piers. From statistic aspect, the fragility analyses illustrate that the bridge isolated by MVFPIs exhibits better seismic performance than that of the bridge isolated by FPBs.