Abstract: Considering the significant influences imposed by the “Internet ” on the composition and operation mode of agricultural product supply chain, it is very beneficial to improve the supervision and quality of agricultural products by building a quality supervision system of the influences imposed by the “Internet ” on agricultural product supply chain. Based on the systematic analysis of the innovation-driven structure and operation mode of agricultural product supply chain under the influence of the “Internet ”, this paper constructed an agricultural product supply chain structure with “Internet ” and analyzed its operation modes, characteristics, and invisible quality problems. Results show that agricultural product supply chain with “Internet ” is helpful to save resources, to improve consumers’ health, and to optimize product structure. Its characteristics include the diversity of participants, the multiplicity of game relationships, and the multiple sources of quality problems. The structure also has some problems such as the lower quality of product itself, degraded quality environment caused by speculation, and negative quality behaviors by low information service. This research indicates that the integrated quality supervision system of “3 1”, including quality supervisions of production sector, marketing sector, and logistic sector, with one integrated virtual information service network can improve the systematic quality supervision significantly. To realize the real benefits of the agricultural product supply chain with “Internet ”, this research suggests to build a unified network platform, to improve the cold distribution system, and to enhance the design of quality contracts.