With the rapid increase of photovoltaic (PV) penetration and distributed grid access, photovoltaic generation (PVG)-integrated multi-area power systems may be disturbed by more uncertain factors, such as PVG, grid-tie inverter parameters, and resonance. These uncertain factors will exacerbate the frequency fluctuations of PVG integrated multi-area interconnected power systems. For such system, this paper proposes a load frequency control (LFC) strategy based on double equivalent-input-disturbance (EID) controllers. The PVG linear model and the multi-area interconnected power system linear model were established, respectively, and the disturbances were caused by grid voltage fluctuations in PVG subsystem and PV output power fluctuation and load change in multi-area interconnected power system. In PVG subsystems and multi-area interconnected power systems, two EID controllers add differently estimated equivalent system disturbances, which has the same effect as the actual disturbance, to the input channel to compensate for the impact of actual disturbances. The simulation results in MATLAB/Simulink show that the frequency deviation range of the proposed double EID method is 6% of FA-PI method and 7% of conventional PI method, respectively, when the grid voltage fluctuation and load disturbance exist. The double EID method can better compensate for the effects of external disturbances, suppress frequency fluctuations, and make the system more stable.