Under non-ideal grid operating conditions such as unbalanced grid voltage and harmonic grid that are commonly found in microgrid conditions, the negative sequence components of the microgrid voltage interfere with the active and reactive current controls in the power conversion system, leading to an increase in the harmonic content of the grid-side current and affecting the power quality of the microgrid system. To solve these problems, firstly, the mathematical model of the LCL-type power conversion system is analyzed, and a linear active disturbance rejection control based on model compensation is designed. Secondly, the influence of non-ideal power grid conditions on the control of the LCL-type power conversion system is analyzed, and the active disturbance rejection control strategy of the LCL-type power conversion system based on frequency-locked loops with harmonic cancellation modules (HCM-FLL) is proposed, which speeds up the system, improves the system’s robustness, and reduces the harmonic content of the network measurement current under the condition of power grid voltage unbalance and harmonic power grid. Finally, by using the verification of MATLAB/Simulink simulation, the current power quality obviously under the condition of voltage unbalance and harmonic power grid is evidently improved by the proposed control strategy. When compared to the traditional control methods, the control strategy proposed in this study features a simple control structure, making it easy to implement in engineering without requiring high controller performance or additional circuits. This reduces design costs and provides a wide range of controller parameters, ensuring strong anti-interference performance without the need for frequent controller parameter adjustments.