The invention relates to a lithium ion battery silicon-based composite anode material, a preparation method of the lithium ion battery silicon-based composite anode material, and a battery. The lithium ion battery silicon-based composite anode material adopts an embedded composite core-shell structure, a core has a structure formed by embedding nano silicon particles into a gap of an inner layer of hollowed graphite, and a shell is made from a non-graphite carbon material. According to the silicon-based composite anode material, mechanical grinding, mechanical fusing, isotropic compression processing and carbon coating technologies are combined, so that the nano silicon particles can be successfully embedded into the inner layer of the graphite and the surfaces of graphite particles are uniformly coated; the high-performance silicon-based composite anode material is obtained and is excellent in cycle performance (the 300-times cycle capacity retention ratio is more than 90%) and high in first efficiency (more than 90%); in addition, the silicon-based composite anode material is high in specific energy and compaction density, and can meet the requirements of a high-power density lithium ion battery; the preparation process is simple, the raw material cost is low, and the environment is protected.