With the popularization and maturity of Internet technology, it has become an inevitable trend of agricultural development to transform the way of agricultural development and connect the Internet with agricultural products. The development of “Internet + agriculture” is rearranging the entire agricultural product industry chain and it also affects the direction of agricultural development. In this article, we make full use of Internet technology, aiming at the development status of the agricultural product industry chain, and design a layer-by-layer inversion model based on partial differential equations to construct an “Internet +” agricultural product industry chain optimization system. This research strives to achieve the coupling of hardware infrastructure and software service systems. A system platform consisting of one platform, two modules, five services, and twelve functional submodules is designed, and a layer-by-layer inversion method of partial differential equations is introduced. The optimization of the agricultural product industry chain from the control of the production side and the sales side is realized. On this basis, further analysis of the accuracy of partial differential equations, system response time, greenhouse climate change control, agricultural product production capacity, and brand value are further analyzed. The following five conclusions are drawn: first, the response time of each interface is 1 to 2 seconds and in the interval of 500 milliseconds, the intensive range is the densest, and the system performance is further improved. Second, for the three spatial fractional partial differential equations, the equations used in this system basically achieved the best accuracy results. Third, at 13: 00, the maximum temperature difference between indoor and outdoor is 6.3°C, which is the moment when the outdoor solar radiation is strongest. The average temperature in the greenhouse is higher than that outdoors, and the trend of the two changes is the same. Fourth, after the optimization of the industrial chain, the highest utilization rate of agricultural product production capacity is 97% and the net profit can reach 150%. Fifth, the brand value of agricultural products has increased from 560 million Yuan in 2010 to 3.153 billion Yuan in 2020, and the quality value has achieved rapid growth. The results show that the “Internet +” agricultural product industry chain optimization system in this article has a reasonable structure, stable operation, easy expansion, and strong applicability and further accelerates the process of modern agriculture.