Understanding the dynamics of ions in the magnetron sputtering process of transparent conductive oxide (TCO) films is essential for clarifying the mechanisms of sputtering-induced damage and developing effective suppression strategies. In this work, indium tin oxide (ITO) is used as a cathode target in an RF magnetron sputtering system operating under pure argon atmosphere, and a positively biased auxiliary anode is introduced to modulate the plasma potential and investigate its effect on the ion energy distribution functions (IEDFs) at the substrate position. The ion energy spectra are measured using a commercial energy–mass spectrometer (EQP 1000, Hiden), and the plasma parameters such as potential and electron density are characterized using a radio-frequency compensated Langmuir probe. The results show that the incident positive ions consist mainly of O⁺, Ar⁺, In⁺, Sn⁺, as well as multiple metal oxide molecular and doubly charged ions. Their energies are determined by the combined effects of the initial ejection or backscattering energy of sputtered particles and the plasma potential. Increasing the auxiliary anode bias leads to an elevation of the plasma potential, thereby enhancing both the kinetic energy and flux of positive ions. In contrast, negative ions such as O^– and $\rm O_2^-$ originate predominantly from cathode sputtering, exhibiting broad, multi-peaked energy distributions that are strongly influenced by RF oscillations of the cathode voltage and plasma potential, as well as relaxation effects during ion transport. Heavier metal oxide negative ions ($\rm InO^-, \;InO_2^-,\; SnO^-,\; SnO_2^-$) respond more slowly to RF sheath modulation, with their high-energy peaks converging toward the cathode bias potential. Applying a positive auxiliary anode bias effectively reduces the cathode bias voltage, thereby suppressing the high-energy tail of negative ions without significantly affecting their total energy-integrated intensity. This demonstrates that auxiliary anode biasing provides an effective means for adjusting the ion energy distributions in magnetron sputtering discharges. The proposed approach provides a potential pathway for mitigating sputtering-induced damage and improving the structural and electronic quality of ITO films. Future work will focus on correlating the measured ion energy modulation with comprehensive film characterizations—including optical, electrical, and interfacial analyses—to further verify the physical mechanisms and evaluate the practical effectiveness of damage suppression during TCO deposition.