The invention discloses a fractional order sliding mode control method of a flexible joint mechanical arm. To overcome buffeting and problems on trace tracking control about integral order sliding mode dynamics control of flexibility of a mechanism arm, the method is as follows: through advantages of sliding mode variable structure control, a fractional order calculus theory is introduced, and a novel fractional order sliding mode variable structure controller high in robustness and interference resistance and having a better buffeting weakening effect is provided by means of quick convergence, information memory and heredity of fractional order differential operators, so a joint flexibility dynamics control system of the mechanical arm exhibits better continuity, rapidity, robustness andgood interference resistance. Finally, the design of a fractional order sliding mode variable structure control method is realized.