Boron-doped isotropic pyrolytic carbon (pyrocarbon) was prepared by CVD using CH4+BCl3+H2 as gaseous precursors. Microstructure of the deposited pyrocarbon on a graphite substrate was investigated using X-ray diffraction, X-ray photoelectron spectroscopy, polarized light microscopy, and scanning and transmission electron microscopy. It was found that the boron-containing pyrocarbon prepared exhibits a multi-scale structure, different from the pure isotropic pyrocarbon deposited under nearly the same experimental conditions. The multi-scale structure consists of carbon agglomerates of fine wrinkled graphitic sheets which contain substitutional boron and some micrometer-sized boron carbide particles uniformly distributed in the carbon agglomerates. Influence and mechanism of boron co-deposition during CVD process are also discussed.