Geometric errors directly affect the tool tip position, reduce machining accuracy, and are one of the most important errors of multi-axis machining tool. However, the geometric errors are intercoupling, and the measured values at different points vary and are stochastic. The identification of the most crucial geometric errors and the determination of a method to control them is a key problem to improve the machining accuracy of machine tool. To achieve this goal, a new analytical method, to identify crucial geometric errors for a multi-axis machine tool is proposed here based on multibody system (MBS) theory and global sensitivity analysis. The volumetric error modeling of multi-axis machine tool has been given by MBS theory, which describes the topological structure of multibody system simply and conveniently in a matrix. The stochastic characteristic of geometric errors is taken into consideration and Sobol global sensitivity analysis method is introduced to identify crucial geometric errors of machine tool. A vertical machining center is selected as an illustration example. The analysis results reveal that the analytical method presented in this paper can identify the crucial geometric errors and are helpful to improve the machining accuracy of multi-axis machine tool.