Under the current trend of power electronics in energy systems, a high percentage of renewable energy transports clean energy to the grid through grid-connected inverters. The pulse-width modulation (PWM) technique brings high-order harmonics near to the switching frequency, and LCL filters with low-pass characteristics become the common choice for grid-connected inverters. However, the low-order harmonics caused by nonideal switching characteristics are difficult to filter out, and the new resonance point introduced by the LCL filter causes a security problem for the energy systems. Firstly, the generation mechanism of the 6 k ± 1 order harmonic and high-frequency resonance from a PV grid-connected inverter is analyzed. Then, a virtual resistor is constructed by the active damping method to absorb the resonant component. Meanwhile, this paper also presents an adaptive modulation voltage compensation method to decrease the low-order harmonics. Finally, the actual measured data of user photovoltaic (PV) and multiple comparative simulations verify these theories. Simulation results show that the proposed coordinated control algorithm reduces the peak of the resonance point, and the rate of low-order harmonics mitigation is more than 50%. The proposed method is suitable for various operating conditions.