In order to improve the geometric accuracy of computer numerical control (CNC) machine tools, the mathematical model for geometric error of CNC machine tools was established. Meanwhile, selecting the five dimensional (5D) laser interferometer XD5LS from API company, then according to the ISO2302:2006 standard, the 5 items of geometric errors were gotten at one measurement time. At last, during actual experiments, a compensation method was put forward for the three axis CNC machine tool which was based on SINUMERIK 840D system. Experimental results show that the geometric error compensation method for the three axis CNC machine tool is simple, effective and easy to realize.