Flexure hinges based micro-displacement structure has been widely used for micro-precision machinery, and the natural frequency characteristics analysis is one of the most important elements in the structure design. In this paper, natural frequency characteristics analysis of a micro-displacement structure with parallel flexible hinges is presented. The effects of each structure parameter to the natural frequency of the micro-displacement structure are simulation by dynamics modeling. The parameters can be divided into three categories, namely, parallel flexure hinges parameter, micro-displacement structure parameter and material parameter. Two micro-displacement structures using common materials are machined for frequency test. The test results of two micro-displacement structure verified the modeling analysis, and the natural frequency characteristics analysis in this paper can be referenced in micro-displacement structure design.