In view of the inefficiency resulting from modular exponentiation of large numbers in the generation process of counterfeit-proof two-dimensional codes by using RSA algorithm, the modular exponentiation of large numbers can be transformed into the small integer stage parallel modular exponentiation by taking advantage of GPU in the multi-threading parallel computing process. The fractional decimals can be processed by adopting the multi-threading technique, with the final calculation result merged together, to generate the corresponding counterfeit-proof two-dimensional code. A comparison has been made between the generation time of the two-dimensional codes before and after they are improved. The experimental results show that the improved scheme helps to improve the efficiency of the two-dimensional code system effectively.