In the applied magnetic field different magnetic intensities in the permanent magnet were introduced between the substrate and target, so as to study their influence on the properties of silicon thin films with light trapping structure prepared by R.F. magnetron sputtering. The microstructures, surface morphology and optical properties of the films were characterized by X-ray diffraction, atomic force microscope (AFM) and ultraviolet spectrophotometer separately. Results show that the silicon nitride thin films are still in amorphous state although an magnetic field was applied on them; however, when the magnetic field in the center is of 1.5 T, the surface morphology of the films has dramatically changed to a special peak structure, i.e. pyramid-like protuberances which are perpendicular to the basal surface; meanwhile, in the visible and near infrared range, the average transmittance of the sample is the highest, which is more than 90%, nearly twice as much as the transmittance of the sample without applied magnetic field, thus the light trapping effect is the great.