The invention discloses a formaldehyde-free soybean protein based adhesive and a preparation method thereof. The adhesive is prepared from soybean meal, bromelain, bean chitinase, dispersion medium water, sodium periodate, diethylenetriamine, glutaraldehyde diglycidyl ether and a curing agent. According to the formaldehyde-free soybean protein based adhesive obtained with the preparation method, soybean meal molecules are degraded, modified and recombined to form a prepolymer, proteins stretch sufficiently, molecular active groups are increased obviously, reactivity, solubility, water-retention and toughness are improved, and after addition of an elastomer-based curing agent, the prepared adhesive has high flexibility, water-resistant adhesion and stability; the requirement of an artificial board adhesive for water resistance can be met, cost of the adhesive is reduced due to reduction of use quantity of a crosslinking agent, and practicability of the protein based adhesive is guaranteed.