The invention relates to the technical field of lithium ion battery carbon cathode materials and in particular to a modified microcrystal graphite cathode material of a lithium ion battery as well asa preparation method and application thereof. The material has the advantages that (1) a modified core-shell structured natural graphite cathode material with artificial graphite embedded into and onthe surface of natural graphite in situ is prepared, the overall structural properties of natural microcrystal graphite are maintained, pores of the natural microcrystal graphite is filled with the artificial graphite, and the outer surface of the natural microcrystal graphite is wrapped by the artificial graphite; (2) compared with a conventional cathode material, the cathode material prepared byusing the method provided by the invention is good in isotropy, is capable of inhibiting and absorbing expansion of electrodes in the charge and discharge process, is high in primary coulombic efficiency, long in service life and good in high-magnification charge and discharge performance and is capable of replacing artificial graphite to manufacture cathode materials of power batteries, so as tolower the cost greatly; and (3) the method is simple in preparation process, low in cost and relatively high in practicability.