After the long period operation on the vertical machining centre, the units which are made up of headstock and spindle system will produce thermal deformation, which affects the precision of axial size of the parts to be machined. By using VMC750 vertical machining center as the experimental objects, the multi-point temperature of the headstock and the spindle elongation deformation were measured to determine the main reason of the spindle deformation. The error compensation model was established, and via the real-time compensation experiment on the thermal error was made during the process of vertical machining center. The results show that the error can be reduced by about 75% by the heat deformation compensation, and the thermal deformation measurement of spindle system on site is 0.028~0.033 mm, which verifies validity of the model.