The laser tracker is an effective instrument for measuring 3D relative displacement in a work volume because its attitude can be freely changed. This paper presents a novel principle to realize the precise calibration of a numerical control (NC) machine tool accurately and quickly; this is the ‘pose measurement principle’, for measuring errors. We also introduce an algorithm for identifying geometric deviations. A NC precise table mounted on a motion axis and a laser tracker are used for the coordinate determination of three fixed points to obtain the pose information of each motion axis, then calculate the pose deviations, and finally identify all the errors. For the error identification, first, according to the definition of geometric errors, we extend the concept of pose deviations, and represent the six geometric errors using a position deviation vector and attitude deviation vector. Next, we geometrically identify the three angular errors and linear errors in order; the error mathematical model for the linear axis and rotary axis are developed, respectively. Moreover, the validity of the calibration algorithm for the base station, measuring points and identification of errors are confirmed by simulations. In the end, the proposed method is applied to a three-axis NC milling machine tool and a rotary table, and then the geometric deviations are identified successfully in 3 h and 2.5 h, respectively. Comparative experiments by means of other instruments also agree well with the proposed method. Thus, the proposed method can be applied to the measurement of the multi-axis machine tool.