Hybrid power systems concerning wind farms have witnessed significant dynamic characteristic changes due to unpredicted generation output and integration mode conversion between frequency-sensitive wind plants and non-scheduled ones. This work presents a robust fractional-order load frequency control (LFC) method for a multi-area hybrid power system in the presence of wind penetration uncertainties. To characterize the injection effect of wind farms, the power system is described by a model with an uncertain wind penetration factor in a pre-estimated range. Then, an enhancement of Levy’s identification method is developed to convert this model into a fractional-order reduced structure to design the load frequency controller, which is in a form of fractional-order PID with a filter for ease of engineering implementation. The closed-loop stability is analyzed by the stability boundary locus (SBL) method under different wind penetration levels. It is shown that superior frequency response performance and system robustness can be obtained if the controller is designed in terms of the model with the worse-case wind penetration. Illustrative examples including a three-area hybrid power system under a variety of wind penetration variations are given to show the effectiveness of the proposed method.