To improve the machine tool accuracy, an integrated geometric error identification and prediction method is proposed to eliminate the positioning inaccuracy of tool ball for a double ball bar (DBB) caused by the rotary axis’ geometric errors in a multi-axis machine tool. In traditional geometric errors identification model based on homogenous transformation matrices (HTM), the elements of position-dependent geometric errors(PDGEs) are defifined in the local frames attached to the axial displacement, which is inconvenient to do redundance analysis. Thus, this paper proposed an integrated geometric error identification and prediction method to solve the uncertainty problem of the PDGEs of rotary axis. First, based on homogeneous transform matrix (HTM) and multi-body system (MBS) theory, The transfer matrix only considering the rotary axes is derived to determine the tool point position error model. Then a geometric errors identification of rotary axis is introduced by measuring the error increment in three directions. Meanwhile the geometric errors of C-axis are described as position-dependent truncated Fourier polynomials caused by fitting discrete values. Thus, The geometric error identification is converted to the function coefficient. Finally, the proposed new prediction and identification model of PDGEs in the global frame are verified through simulation and experiments with double ball-bar tests.