The integration of renewable energy sources (RESs) into power systems, particularly in microgrids, is becoming a prominent trend aimed at reducing dependence on traditional energy sources. Replacing conventional synchronous generators with grid-connected RESs through power electronic converters has significantly reduced the inertia of microgrids. This reduction negatively impacts the dynamics and operational performance of microgrids when confronted with uncertainties, posing challenges to frequency and voltage stability, especially in a standalone operating mode. To address this issue, this research proposes enhancing microgrid stability through frequency control based on virtual inertia (VI). Additionally, the Iterative Learning Control (ILC) method is employed, leveraging iterative learning strategies to improve the quality of output response control. Accordingly, the ILC-VI control method is introduced, integrating the iterative learning mechanism into the virtual inertia controller to simultaneously enhance the system’s inertia and damping coefficient, thereby improving frequency stability under varying operating conditions. The effectiveness of the ILC-VI method is evaluated in comparison with the conventional VI (C-VI) control method through simulations conducted on the MATLAB/Simulink platform. Simulation results demonstrate that the ILC-VI method significantly reduces the frequency nadir, the rate of change of frequency (RoCoF), and steady-state error across iterations, while also enhancing the system’s robustness against substantial variations from renewable energy sources. Furthermore, this study analyzes the effects of varying virtual inertia values, shedding light on their role in influencing response quality and convergence speed. This research underscores the potential of the ILC-VI control method in providing effective support for low-inertia microgrids.