The invention discloses a silicon-carbon composite material and a preparation method thereof, and a lithium ion battery. The preparation method comprises following steps: (1) coating a silica-based material with a transition layer to obtain the transition layer-coated silica-based material; (2) coating the transition layer-coated silica-based material with carbon to obtain a carbon-transition layer-silicon based composite material; and (3) removing the transition layer to obtain the silicon-carbon composite material. The silicon-based material is coated with the transition layer, the transition layer is coated with the carbon, and the transition layer between the silicon-based material and the carbon is removed, so that a plurality of pores are formed between the silicon-based material and the carbon of the silicon-carbon composite material. The size of the pores between the silicon-based material and the carbon can be controlled precisely by setting the thickness of the transition layer according to micro-volume expansion theoretical value of the silicon-based material when lithium is embedded, so that volume effect of the silicon-carbon composite material is reduced effectively, and cycling performance of the lithium ion battery is further enhanced. The carbon of the silicon-carbon composite material is capable of increasing conductivity and rate capability of the composite material.