With the continuous development of the logistics industry and big data technology, the integration of traditional industries and the Internet of Things has become the trend of the times. However, agricultural product quality problems occur from time to time in multiple links such as the production and circulation of agricultural products. Therefore, the agricultural product supply chain based on the Internet of Things has gradually received attention. The purpose of this paper is to study the application of perception data fusion of agricultural products supply chain based on internet of things. In order to study the application of perception data fusion of agricultural products supply chain based on Internet of things, this paper analyzes the status quo of agricultural products industry traceability platform and extracts other product supply modes based on the Internet of things technology. After analysis and comparison, it comes to the perception data fusion mode suitable for the agricultural product supply chain, and uses the information technology based on the internet of things to carry out the agricultural product circulation process Internet of things transformation and process optimization. The results show that the application of data fusion based on the internet of things can solve 69.45% of the agricultural products whose origins are unknown and cannot be traced, improve the supply efficiency of agricultural products by 43%, reduce the health problems of agricultural products by 31.24%, reduce the prices of agricultural products by 13%-20%, improve the logistics efficiency and save about 5 million tons of agricultural products. Therefore, it is necessary to study the application of agricultural product perception data fusion based on internet of things.