The invention relates to a machining thermal deformation prevention cutting method for machining of a long ship screw shaft with the length being 22 m. The method comprises the steps that plugs are mounted at the two ends of a screw shaft through hole; the middle section position of the screw shaft is sleeved with a transition sleeve, and two centres are used for clamping; a center frame is built, machining frame position gears are turned at the two sides of the center frame, and machining frame positions are set; the center frame is adjusted till it is detected that runout of each machining frame position is within 0.1 mm, then cutting machining is carried out, and during cutting, the rotating speed of a spindle is 25 turns/min, the feed quantity is 0.2 mm/turn, and the single-side cutting parameter is 2 mm; and runout of the transition sleeve is readjusted to be within 0.015 mm, the machining frame positions are re-turned, abrasive machining is carried out after the allowance of 0.2 mm is reserved according to the drawing size, and the total runout of the outer edge of the screw shaft is checked. The method has the beneficial effects that in the process of carrying out cutting machining, the rotating speed of the spindle is 25 turns/min, the feed quantity is 0.2 mm/turn, the single-side cutting parameter is 2 mm, and therefore the thermal deformation phenomenon can be effectively avoided during cutting machining when cutting is carried out according to the cutting parameter.