The structures and anode performance of graphitized and boron-doped milled mesophase pitch-based carbon fibers (mMPCFs) have been comparatively studied and the results obtained by X-ray diffraction (XRD), SEM, Raman spectroscopy and electrochemical measurements are discussed. The boron doping at the level of 2.66 at.% (2.4 wt.%) enhances the growth of the crystallite thickness, Lc(002), of the host mMPCF. The B-doped mMPCFs show a strong Raman peak near 1365 cm−1, and a well-defined peak at 1620 cm−1. The E2g2 graphite Raman band at 1580 cm−1 is shifted to 1590 cm−1 due to B-doping. On the basis of the integrated intensity ratio R(ID/IG), it is suggested that the substitutional boron in the mMPCFs is homogeneously distributed within the graphene layer in the fiber form. Boron doping leads to about an 11% increase in charge capacity and also an improved cyclic efficiency. The electrochemical Li intercalation takes place at a higher voltage in boron-doped mMPCFs than in undoped mMPCFs by about 40 mV, presumably because the substitutional boron acts as an electron acceptor in the graphite lattice as well as affecting the exposed dislocation edge-type surface.