A multibody dynamic model is developed for dynamic analysis of a 5-DOF flexure-based nanopositioning stage in the projection optical system of the semiconductor lithography in this paper. The 5-DOF stage is considered as an assembly of rigid bodies interconnected by elastic flexure hinges. Considering the length effects of flexure hinges, multibody dynamic equations are established according to spatial motions of rigid bodies by using Lagrangian method. The shear effects and the torsional compliances of the commonly used circular flexure hinges are considered to enhance the modeling accuracy. The accuracies of various out-of-plane compliance formulas are also discussed. To verify the developed dynamic model, the finite element analyses (FEA) by using ANSYS and modal hammer experimental tests of the primary flexure-based composition structures and the integral 5-DOF stage are performed. The analytical modal frequencies are well in agreement with FEA and experimental test. The results are significant to analyze and optimize the 5-DOF flexure-based nanopositioning stage.