A natural graphite-based modified composite material, a preparation method therefor, and a lithium ion battery comprising the modified composite material. The natural graphite-based modified composite material comprises natural graphite and non-graphitized carbon coated on the inner and outer surfaces of the natural graphite. The preparation method comprises: (1) subjecting spherical natural graphite to isotropic treatment; (2) performing granularity control and shaping treatment; (3) subjecting the inner surface and the outer surface of the material obtained in step (2) to simultaneous modification; and (4) performing carbonization, so as to obtain a natural graphite-based modified composite material.