In this work, X-ray diffraction (XRD), coulometry titration, X-ray photoelectron spectroscopy (XPS) and electron spin resonance (ESR) were used to study the structure of lithium-intercalated pyrolytic poly (furfural alcohol) (PFA) and mesophase carbons formed at 1000 °C (MCMB1000) and 2800 °C (MCMB2800), respectively. The effect of phosphorus doping on the intercalation capacity was identified through a comparison between PFA and MCMB 1000. It was further verified by a separate experiment, in which MCMB 1000 was treated with phosphoric acid followed by heat treatment at 1000 °C. The maximum lithium intercalation concentration x ( x in Li x C 6) increased sharply with the introduction of phosphorus, whereas it was not reflected in XRD. Although there were two turning points in the open circuit voltage E-x curve of PFA, no staging phenomenon could be observed. A simple model based on mean field theory was used to investigate the effect of the attractive interaction between intercalates on the formation of lithium ordering in the structure of the intercalation compound. It was inferred from the XPS spectra that PFA showed a better ability to accept electrons than MCMB1000, although they have similar crystalline structures. The XPS spectra of Li-PFA also indicated partial covalent property of the Li-PFA interaction, which was further confirmed by ESR data. The influence of crystalline and electronic structures of carbon on lithium intercalation capacity was demonstrated.