In the present study, the sputtered aluminum nitride (AlN) films were processed in a reactive pulsed DC magnetron system. We applied a total of 15 different design of experiments (DOEs) on DC pulsed parameters (reverse voltage, pulse frequency, and duty cycle) with Box–Behnken experimental method and response surface method (RSM) to establish a mathematical model by experimental data for interpreting the relationship between independent and response variables. For the characterization of AlN films on the crystal quality, microstructure, thickness, and surface roughness, X-ray diffraction (XRD), atomic force microscopy (AFM), and field emission-scanning electron microscopy (FE-SEM) were utilized. AlN films have different microstructures and surface roughness under different pulse parameters. In addition, in-situ optical emission spectroscopy (OES) was employed to monitor the plasma in real-time, and its data were analyzed by principal component analysis (PCA) for dimensionality reduction and data preprocessing. Through the CatBoost modeling and analysis, we predicted results from XRD in full width at half maximum (FWHM) and SEM in grain size. This investigation identified the optimal pulse parameters for producing high-quality AlN films as a reverse voltage of 50 V, a pulse frequency of 250 kHz, and a duty cycle of 80.6061%. Additionally, a predictive CatBoost model for obtaining film FWHM and grain size was successfully trained.