The small-size microstructure models of the 3D needled waste cotton fiber/epoxy composites (3DNWCFCs) were brought out to predict their key vibration parameters (natural frequency and mode shapes) with the finite element analysis method. Six kinds of 3DNWCFCs with different parameters were prepared and tested by the experimental modal analysis method to verify the accuracy of the prediction of the natural frequencies and mode shapes with the finite element method. The effects of the fiber volume content and needling density of the composites on the modal behavior were investigated. The natural frequency of the cantilever beams of the composites increased with the increase of the fiber volume content and increased at first then decreased with the increasing needling density. The effect of needling density on the vibration properties of the composite depended on the degree of damage and entanglement of Z-direction fibers. The comparative analysis of the finite element analysis and the experimental results showed that the small-size microstructure models of the 3DNWCFCs were effective to predict their vibration parameters. Therefore, the small-size finite element models can be used to predict the modal properties of the staple fiber reinforced composites effectively with less time and lower economic costs.