Thin films consisting of silicon nanocrystals fabricated by high silicon content in silicon rich oxide show unique properties of decreasing resistivity and increasing light absorption while maintaining quantum confinement effects. With that said, the effect of the annealing temperature and doping element on the microscopic structure of silicon nanocrystals (Si NCs) and the film are still under research. In this study, individual intrinsic, boron-, and phosphorus-doped films are annealed at various temperatures, and their structural properties are analyzed via atom probe tomography together with glancing incidence x-ray diffraction, Raman spectroscopy (Raman), transmission electron microscopy (TEM), and energy filtered TEM. In addition, photoluminescence (PL) is performed and linked with their microstructural properties. The Si NC growth is confirmed at annealing temperatures of 1000 °C and 1100 °C. The microstructure of the Si NCs in the whole film is dramatically changed by increasing the annealing temperature from 1000 °C to 1100 °C. In addition, doping changes the arrangement of the Si NCs by assisting their penetration across the SiO2 barrier layers. This study helps to understand the relationship between the microscopic and macroscopic properties of the Si NC film, showing that the size and distribution of the Si NCs are correlated with the obtained PL profiles.