Traditional agricultural products supply chain information systems face several problems, such as information asymmetry, tracing difficulty, and insufficient data security, which can be efficiently solved using blockchain technology due to its decentralized, non-tampered, and highly transparent characteristics. Accordingly, the application of blockchain technology in the agricultural products supply chain information system was comprehensively evaluated in this study. A comprehensive evaluation index system for the agricultural products supply chain information system was established based on blockchain technology, a mathematical model of AHP–CRITIC–TOPSIS was constructed to comprehensively evaluate supply chain information system, and an empirical study was carried out on 18 agricultural products enterprises in China. Results show that blockchain technology can significantly improve the performance of agricultural products supply chain information systems and enhance the efficiency and transparency of supply chains, and the AHP–CRITIC–TOPSIS mathematical model can be used to assess the collaboration efficiency among enterprises in this system. This study offers great reference value for promoting the digital transformation and intelligent upgrading of agricultural products supply chains, thus helping the government and supervision departments in actively supporting the application of blockchain technology and promoting a healthy development of agricultural products supply chains.