Aiming at the deficiencies in the practical teaching scene of supply chain management majors in higher vocational colleges and universities, this paper proposes a scene creation method based on the integration of industry and education and virtual simulation. Virtual simulation from the logistics machinery intelligent operation and maintenance and supply chain risk early warning two aspects to realize. Among them, the intelligent operation and maintenance system of logistics machinery is constructed by using Omniverse and Isaac Sim, and the simulation of supply chain risk early warning is realized by changing parameters in a relatively stable supply chain system. The research finally creates practical training teaching scenarios based on MR and VR technologies for the reform of supply chain management professional practice teaching in higher vocational colleges. When the intelligent operation and maintenance system of logistics machinery designed in this paper carries out virtual simulation actions, the delay time of the actions is less than 2s, and the detection accuracy of the supply chain risk early warning system is above 90%. Students’ acceptance of practical training teaching based on industry-teaching fusion and virtual simulation is high, and this teaching mode can not only better meet the requirements of skill development, but also promote the reform of supply chain management professional practice teaching in higher vocational colleges and universities to a certain extent.