Nanocrystalline silicon (nc-Si:H) films with an average grain size ranging between 2 and 10 nm are prepared in a modified plasma chemical vapor deposition system. X-ray diffraction, transmission electron diffraction, and high resolution electron microscope are used to elucidate the structural nature in the deposited nc-Si:H films. The lattice network of the deposited silicon films changes from disordered structure to ordered structure with the increasing of plasma energy. The results also show that the crystal lattice of the nc-Si:H film is distorted from those of microcrystalline silicon and crystalline silicon. In the observed x-ray diffraction, there are two anomalous peaks at 2θ = 29.5° and 32.5° of Si besides the normal peaks at 2θ = 28.5° of Si(111) and 2θ = 47.3°of Si(220). By the high resolution electron microscopy study, a new crystallography structure with distorted Si(111) crystallites in nc- Si:H films is found. Based on our results, a structure model of nc-Si:H films is proposed.