The planar defect behavior and phosphorus (P) diffusion of P-doped silicon (Si) thin film on monocrystalline Si with annealing was investigated by high-resolution transmission electron microscopy. These images indicate that the as-deposited Si thin film crystallizes with many planar defects, such as stacking faults and twin boundaries. Secondary ion mass spectroscopy and atom probe tomography reveal that P atoms are segregated to the planar defects and diffuse out the Si substrate at 600 C. The solubility of P atoms has an influence on the rearrangement of Si atoms, which leads to the annihilation of the defects in the deposited Si thin film.