Understanding the distributions and behaviors of dopants in Si nanocrystal are the primary and necessary issues to realize the controllable doping at nanoscale and develop the next generation of optoelectronic devices. This work reports the atomic-scale distributions of phosphorus and boron dopants in Si nanocrystals multilayers. The phosphorus-doped and boron-doped Si nanocrystals/SiO2 multilayers are fabricated by PECVD and subsequently annealed at 1000 °C. It is found that the locations of phosphorus are redistributed after the formation of Si nanocrystals due to the combined effects of formation energy and self-purification. Phosphorus dopants are mainly distributed at the Si nanocrystals surfaces to passivate the dangling bonds, while part of them incorporate into Si nanocrystals lattice sites to provide free electrons. However, boron dopants exhibit different distributions in contrast to phosphorus. The concentration of boron on Si nanocrystals surfaces can reach as high as 40.0 at. %, which forms a dopant-shell covering on Si nanocrystals. Meanwhile, the boron dopant-shell can modify the surface states of Si nanocrystals like Si-oxide related emission centers and dangling bonds, which is responsible for the luminescence properties. Moreover, the boron-aggregations with concentration near 74.8 at. % are appeared inside Si nanocrystals and led to the damage of crystalline lattice.