The effects of a magnetic field perpendicular to a discharge electric field (cross-magnetic field) and their modulation phase are discussed in a plasma enhanced chemical vapor deposition (PECVD) system as important external control parameters for the preparation of hydrogenated amorphous silicon (a-Si:H) using silane (SiH4) plasmas. In this paper, a-Si:H thin films are prepared under the conditions of the same and random phase modulations of an electric field (E) and a magnetic field (B). The effects of removal and growth suppression on silicon particles owing to the same phase modulation of E and B fields can suppress the disorder parameter and the surface roughness of the deposited films.