Based on the fact that the inductor and the capacitor are of fractional order in nature, the mathematical model of the fractional order boost converter in pseudo continuous conduction mode is established by using the fractional order calculus theory. Due to the affine non-linear nature in this mathematical model and a similar Lyapunov stability theorem of the fractional order system, a fractional order non-linear controller is designed. On the basis of chain fractance and the improved Oustaloup algorithm, the circuit model of fractional order inductor and capacitor are built. The fractional order controller is verified by the Matlab/Simulink software. Simulation results show that the controller enhances the dynamic and steady-state performance, so as to realize the stability and achieve good dynamic performance of the fractional order system during large fluctuation of power supply and load disturbance.