The microstructure of pyrolytic carbon significantly affects the performance of aircraft brake discs. In this study, to explore the effect of precursor on the microstructure of pyrocarbon, two types of pyrocarbon films were grown on the quartz glass substrates by isothermal isobaric chemical vapor infiltration using methane and acetaldehyde as precursors. The microstructures of both the films and their formation mechanisms were investigated and compared. The thicknesses of the pyrocarbon films from methane and acetaldehyde were approximately 860 nm and 986 nm, respectively. The film from acetaldehyde comprised quite a few carbon nanoflakes with sizes in the range of 100–200 nm. However, the film from methane exhibited lots of small and dense carbon layers, with a large number of carbon particles of about 20 nm size. Compared to the methane deposited film, the lattice fringes of the carbon layers in the acetaldehyde deposited film were more ordered and had a better orientation. Moreover, the acetaldehyde deposited film had fewer defects owing to the higher sp2/sp3 ratio than that of the methane deposited film. This study may provide new insights into the selection of precursors for preparing pyrocarbon.