For energetic deposition, ion bombardment was an important factor independent of grain size for influencing the residual stress, and the energy and flux were critical parameters to determine the residual stress evolution. In this work, Modulated Pulsed Power magnetron sputtering (MPPMS) and Deep Oscillation magnetron sputtering (DOMS) were employed to control the energy and flux to modulate the ion bombardment for intrinsic stress generation under similar average power. The films thickness was selected at 0.1, 0.2, 0.5, 1.0, 1.5 and 3.0 μm to give a comparative study of the intrinsic part of residual stress. All Cr coatings were textured along Cr(110) preferred orientation with dense T-zone columnar microstructure of equivalent grain size. Compared with MPPMS, Cr thin films deposited by DOMS showed a compressive residual stress tendency. When the Cr thin films were under 0.5 μm, Cr thin films deposited by DOMS showed higher compressive residual stress. Further increasing the film thickness, the compressive residual stress first showed a sudden decrease in a sharp slope, and then turn to relative slow decrease and gradually turn to show tensile stress. In the film continuous growing process, the ion bombardment showed limited effect in the early growth stage, but high bombardment effect will directly influence the grain size. At early growth stage, ion bombardment showed limited contribution to residual stress formation. For thick Cr thin films, energy of the bombardment ions relied on residual stress. Ion energy was an important factor influencing the formation of compressive residual stress, and ion bombardment with high energy assisted the generation and control of compressive residual stress.