The structural deviation of boron-doped vapor-grown carbon fibers (VGCFs) with diameters around 10 μm relative to their undoped counterparts was investigated by polarized microprobe Raman spectroscopy and field-omission scanning electron microscopy as a function of heat-treatment temperature (HTT). Boron doping induces the formation of dislocation loops in the surface, which combine into larger loops with increasing HTT. The depolarization ratio, Dp, of the E2g2 mode for VGCFs increases gradually with increasing HTT, and finally approaches the value of highly oriented pyrolytic graphite, which is consistent with the asymmetric shape of the peak at ∼2725 cm−1 in the second-order Raman spectra. On the other hand, the Dp ratios of the E2g2 mode for boron-doped VGCFs show no deviations up to an HTT of 2100 °C, as compared to that of VGCFs, and decrease with increasing HTT, whereas the Dp ratios of the D peak show a maximum value at 2100 °C, and decrease gradually with increasing HTT. Consistent with these Raman results, boron atoms in the graphite lattice introduce a decreased d002 spacing (accelerating graphitization), but also hinder two-dimensional structural development and increase the amount of disorder. This is done by introducing tilt boundaries and vacancies, which make the Dp ratio of the E2g2 mode lower than the value for polycrystalline graphite, even though the fibers are heat treated at 2800 °C.