The invention discloses a fractional order sliding mode variable structure control method of a pneumatic position servo system. The method comprises the steps that firstly, a model of the pneumatic position servo system of a control object is built; secondly, a fractional order sliding mode face of the pneumatic position servo system is built; thirdly, the exponential reaching law of the pneumatic position servo system is set; fourthly, a controller of a fractional order sliding mode variable structure is built, a computer outputs a control signal subject to amplitude limiting to a proportional valve through D/A conversion, the proportional valve controls the pressure of an air cavity side A and an air cylinder side B of a rodless air cylinder, and the displacement y of a piston in the rodless air cylinder is adjusted in real time. The pressure detection hardware or pressure identification and estimation algorithm does not need to be added, and the better tracking effect and the higher control precision can be obtained.