This study analyzes the mechanisms of harmonic resonance formation in distribution systems with high photovoltaic (PV) penetration and its impact on system stability, power quality, and protection reliability. The growing integration of PV units alters system impedance due to inverter-based power electronics, leading to stronger resonance and harmonic interactions. The IEEE 13-bus distribution system was used as a reference model, and MATLAB/Simulink-based simulations were performed to conduct frequency scans, harmonic load flow, and transient analyses under varying PV penetration levels (10%, 30%, 50%). Results show that higher PV ratios cause downward shifts in resonance frequencies, increase total harmonic distortion (THD), and heighten the risk of protection relay malfunctions. Active damping and virtual impedance-based control strategies effectively mitigate these issues, reducing resonance peaks by up to 50%. The study emphasizes the need for coordinated power quality and protection planning in high PV penetration networks.