Boron (B)-doped silicon-rich SiC (SiC_x, 0<x<1) thin films were deposited using magnetron sputtering (MS) and annealed in a tube furnace. The effect of substrate temperature (T_s) on the conductivity and microstructures of the annealed B-doped SiC_x thin films were studied. The crystalline fraction increased by 5%, while the conductivity increased by 10–100 times, in the annealed thin films deposited at about 200 °C, comparing to that deposited at RT −400 °C. The face-centered cubic (fcc) Si nanocrystals (Si-NCs) formed in the surface layer when T_s was about 200 °C. It was suggested that T_s influenced the crystallization, conductivity and even the microstructures of Si-NCs. The proper T_s was helpful to improve the crystallization and conductivity of the B-doped Si-NCs in SiC_x thin film.