In multibody dynamics, differential and algebraic equations which can satisfy both equation of motion and kinematic constraint equation should be solved. To solve these equations, coordinate partitioning method and constraint stabilization method are commonly used. In the coordinate partitioning method, the coordinates are divided into independent and dependent and coordinates. The most typical coordinate partitioning method are LU decomposition, QR decomposition, and SVD (singular value decomposition). The objective of this research is to find an efficient coordinate partitioning method in the dynamic analysis of flexible multibody systems. Comparing two coordinate partitioning methods, i.e. LU and QR decomposition in the flexible multibody systems, a new hybrid coordinate partitioning method is suggested for the flexible multibody analysis.