The slide-film damping effect caused by cavity structures is easily neglected in the design of bulk-micro-machined resonant MEMS device fabrication and packaging processes. On the basis of theory calculations, simulations, and actual tests, in this study, we investigate the cavity-depth effect on 3D wafer-level packaged MEMS resonators with the in-plane-motion mode, in which slide-film damping is dominant. On the one hand, it is found that the slide-film damping coefficient is inversely proportional to the cavity depth and remains stable for the cavity depth above a specific value. The critical cavity depth acquired from theoretical results is ~10 μm, which is distinct from that of ~30 μm from simulation results. On the other hand, the variation tendency of simulation results is more in agreement with those of test results for fabricated devices than the theoretical prediction. Hence, before the structure fabrication for a resonator dominated by slide-film damping, it is imperative to choose a conservative cavity depth with a relatively high value from the combination of theory and simulation analyses, so as to ensure the high or desired Q-factors of fabricated resonators, particularly in wafer-level packaging with the low-vacuum or atmospheric pressure. Overall, this work provides not only an analysis strategy on device cavities’ slide-film damping but also the optimization design of wafer-level packaging structures and processes.