This paper presents an efficient hybrid method for dynamic analysis of a flexible multibody system. This hybrid method is the combination of a penalty and augmented Lagrangian formulation with the mass-orthogonal projections method based on the absolute nodal coordinate formulation (ANCF). The characteristic of the ANCF that the mass matrix is constant and both Coriolis and centrifugal terms vanish in the equations of motion make the proposed method computationally efficient. Within the proposed method, no additional unknowns, such as the Lagrange multipliers in the Newmark method, are introduced, and the number of equations does not depend on the number of constraint conditions. Furthermore, conventional integration stabilization methods, such as Baumgarte’s method. are unnecessary. Therefore, the proposed method is particularly suitable for systems with redundant constraints, singular configurations, or topology changes. Comparing results from different methods in terms of efficiency and accuracy has shown that the proposed hybrid method is efficient and has good convergence characteristics for both stiff and flexible multibody systems.