Precision and ultra-precision machining technology rely mainly on the machine tools’ accuracy. To improve it, the measurement, calculation, prediction and control of geometric errors are critical. The traditional measurement methods have lower precision because of ignoring small angle errors. To obtain complete geometric errors of multi-axis machine tools, this paper proposes a new method of coupling and decoupling measurement. Specifically, we used a laser interferometer and dial indicators to measure 36 items of complete geometric errors of multi-axis machine tools. A homogeneous transformation matrix (HTM) was applied to model the error transfer route. The transfer law of complete errors for each machining point was explored and derived. Furthermore, we selected and calculated integrated errors of 36 machining points. Finally, we proved the correctness of the method by comparing the measurement result of a ball bar test and coupling and decoupling measurement of geometric errors. We found that items of small geometric angle errors have a greater impact on machining accuracy than those of geometric displacement errors. Complete geometric errors measured via the coupling and decoupling measurement method can evaluate integrated errors more precisely and comprehensively.