Cold chain logistics is important for reducing post-harvest losses of agricultural products and ensuring the safety of agricultural products. COVID-19 cases related to cold chains have occasionally occurred, prompting considerable and widespread attention to cold chain logistics. The establishment of an effective traceability system for agricultural products within cold chain logistics is vital for ensuring their safety during the COVID-19 pandemic and achieving accurate traceability and recall. A study was conducted to assess the developmental status of cold chain logistics for China’s agriculture products and identify challenges associated with cold chain logistics in the context of COVID-19. The study highlighted the advantages of blockchain-based traceability of agricultural products within cold chain logistics. Accordingly, a blockchain-based system was constructed for ensuring effective traceability of agricultural products within cold chain logistics extending from the production to the sales areas (i.e., from the field to the table). First, the demand for a traceability system was analyzed in detail from the perspective of the government, enterprises, and consumers. Second, six layers of the system architecture, comprising perceptions, data, networks, and the core, application, and user layers were delineated. Next, a storage mechanism and the system flow were designed and analyzed, and the on-chain and off-chain storage mechanisms of the “Inter Planetary File System+ blockchain” were applied for data storage, thereby addressing the deficiency of the blockchain and improving the operation and query efficiency of the traceability system. Lastly, the main functions of three respective ports for the government, enterprises, and consumers were introduced. This system can effectively resolve various challenges, such as tracing the entire process of cold chain logistics for agricultural products and a lack of clarity regarding assigned responsibility. Thus, the traceability of the entire process of cold chain logistics for agricultural products can be achieved, thereby enhancing the effectiveness of oversight of agricultural production, which ensures the quality and safety of agricultural products and strengthens consumers’ trust in food safety.