The goal of this work is to determine how the rate of Ni deposition affects the structural characteristics that regulate the magnetization of Ni/Al multilayer thin films sputtered on flexible acrylic acetate polymer substrates. The films with a 5[Ni(20nm)/Al(10nm)] structure, were gradually sputtered as different Ni deposition rates in the total thickness of 150 nm. With an increase in the rate of Ni deposition, the Ni contents increased from 61.5% to 69.6%. And, X-ray diffraction analysis verified that the films featured a face-centered cubic structure with variable peak intensities. Also, the scanning electron microscopy surface morphology analyses revealed that variations in the film surfaces were a result of the deposition rates. For magnetic measurements, the differences in the structural analysis were observed to cause a notable variation in saturation magnetization, MS, and coercivity, HC values. Accordingly, MS values increased consistently between 359.0 and 389.7 emu/cm3, but HC values decreased from around 34–32 to 28 Oe with the increase in Ni deposition rate from 0.02 to 0.10 nm/s. It is also observed that when the Ni layers are generated at very fast deposition rates, the Ni/Al multilayer films have a high MS/HC ratio, which is significant for magnetic sensors. It has been concluded that the magnetisation of Ni/Al multilayer thin films can be controlled by the structural properties adjusting the Ni deposition rate.