Silicon oxide films containing nanocrystalline Si (nc-Si) are fabricated by magnetron sputtering method followed by one-step-annealing, two-step-annealing and rapid thermal annealing (RTA), separately. In silicon-rich oxide films containing ～ 42.63 at.% of Si, dense nc-Si in a magnitude of 1012/cm-2 are obtained in all of the samples subjected to three different thermal treatments. In the two-step-annealing sample, the density of nc-Si reachs a maximum (2.2× 1012/cm-2), and the nc-Si is well crystallized and uniform in size distribution. In the one-step-annealing sample, the density of nc-Si is silightly lower than in the two-step-annealing sample, and large deficiently crystallized nc-Si is observed in the sample. The RTA leads to the lowest density of nc-Si with the largest size distribution among the three samples. Moreover, large nc-Si formed by coalescence of small ones and twin crystals are also discovered in the RTA sample. It is believed that nucleation at the early stage of nanocrystal growth influences the density and the micostructure of nc-Si. The annealing at low temperature in the two-step-annealing facilitates the formation of new nulcei, which is beneficial to improving the quality and density of nc-Si.