The experimental study of vortex induced vibration needs to be carried out in water tunnel, but in previous associated simulation work, the water tunnel was treated as an infinite flow field in the depth direction with the effect of the free surface neglected. In the paper, the dynamic characteristics and physical mechanisms of a passive turbulence control (PTC) cylinder in a flow field with a free surface is studied, and the combined technique of a volume of fluid (VOF) method and vortex-induced vibration (VIV) was realized. In the range of Reynolds number studied in this paper (3.5 × 104 ≤ Re ≤ 7.0 × 104), the dynamic parameters (lift and drag coefficients), vortex structures, VIV response (amplitude and frequency ratios), and energy harvesting characteristics of a PTC cylinder under different flow conditions were obtained. The study found that: (1) the shear layer was made more unstable behind the cylinder by the free surface, which made it quicker to reach periodic stability, and the asymmetry shortened the initial stage of vibration of the oscillator, which made it easier to produce dynamic control of the motion of the oscillator; (2) the presence of the free surface only affected the positive amplitude ratio, but had almost no effect on the negative amplitude ratio; (3) the frequency ratio in the free surface flow was closer to the experimental data; (4) the presence of the free surface did not affect the detached vortex pattern in the flow around the stationary cylinder, but in the VIV, the lower the free surface height Z, the more vortices that were shed from the moving cylinder.