The work aims to design a traceability code of fresh fruits to meet consumers' demands for the quality and safety of fresh products. In view of the problems such as ordinary QR codes being tampered and forged, digital signature technology was introduced to increase the number of primes in the algorithm, and the Chinese residual theorem was applied in the signature process to improve the computation efficiency. The Chinese residual theorem was used to solve the existing single radix conversion method and mixed radix conversion method. Combined with Fermat's little theorem, the signature process of RSA under four primes was optimized respectively, and the signature time before and after optimization was compared. Finally, the algorithm was implemented through the Python test algorithm. The signature time under the optimized algorithm was reduced by 83.8% averagely compared with that under the traditional double prime algorithm. The optimized algorithm could resist brute force attacks, choice cipher-text attacks, error attacks and score attacks on different objects in the algorithm. Thus, an anti-counterfeiting traceability code considering efficiency and security is generated, which also provides assurance for consumers in purchasing products.