The invention relates to the technical field of corrugated paper, in particular to composite corrugated paper and a preparation method thereof. The composite corrugated paper comprises first surface paper, an antibacterial layer, a reinforcing layer, corrugated core paper, a fiber layer, a waterproof layer and second surface paper which are sequentially attached, and the upper surface of the reinforcing layer and the lower surface of the fiber layer are each coated with a composite adhesive layer. A composite adhesive is prepared from the following raw materials in parts by weight: 10-20 partsof modified alkyd resin, 0.1-2.0 parts of azo initiator, 1-5 parts of phenolic compound, 10-15 parts of deionized water, 1-5 parts of polyvinyl alcohol, 10-20 parts of rice hull fiber, 20-30 parts ofepoxy resin, 1-3 parts of nano SiO2, 8-12 parts of chitosan, 1-5 parts of plasticizer, 0.1-3.0 parts of curing agent, 0.1-3.0 parts of antioxidant, 0.1-1.0 part of citric acid, 1-5 parts of a fillerand 15-25 part of starch. The composite corrugated paper provided by the invention has good strength and mildew-proof and antibacterial effects, and is long in service life.