In this work, Cu thin films were experimentally fabricated at different target–substrate distances by 2-inch and 4-inch circular planar magnetron targets. Meanwhile, the sputtering deposition of Cu thin films was investigated via an integrated multiscale simulation, where the magnetron sputtering discharge was modeled using the Monte Carlo (MC) method, and the sputtered particle transport was simulated using a coupled Monte Carlo (MC) and molecular dynamics (MD) method. Experimental results indicated that, as the target–substrate distance increased from 30 to 120 mm, the film thickness distribution of the 2-inch target sputtering changed from a bell-shaped curve to a line-shaped curve, while that of the 4-inch target sputtering varied from a saddle-shaped curve to a line-shaped curve. The simulation results were accordant with the experimental results. The simulation results revealed that, at a target–substrate distance of 30 mm, the sputtering particle flow from the 2-inch target overlapped strongly near the substrate center, leading to a bell-shaped film thickness distribution, while the increased diameter of the erosion groove on the 4-inch target reduced the superposition effect of the sputtering particle flow near the substrate center, resulting in a saddle-shaped film thickness distribution. In addition, when the target–substrate distance ranged from 30 to 120 mm, the film thickness uniformity of 4-inch target sputtering was superior to that of 2-inch target sputtering, and the underlying mechanism was discussed in detail.