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Combining the stochastic averaging method and generalized harmonic function, we propose a procedure to investigate the fractional-order energy harvesting system. First, we can obtain the approximately equivalent system by means of the generalized harmonic transformation; Second, the stochastic averaging method is utilized to get the approximate stationary solutions of the simplified system. Finally, In order to illustrate the accuracy of the developed scheme, two examples are carried out. The results show that the developed procedure has a satisfactory reliability. The influences of the intensity of noise excitation, the fractional order, the fractional coefficient and the nonlinear restoring force on the mean-square voltage (MSV) and mean output power (MOP) are also investigated.