With the application of new technologies such as digital twins and AR/VR to flexible manufacturing and other production links, the industrial Internet places a greater demand on the real-time and reliable execution of industrial big data processing, intelligent decision, and production line coordination. Deterministic networking has the potential to satisfy such requirements. However, the current application of deterministic networking is limited to two or three layers, and the round-trip delay involving industrial applications, networks, and edge computing is uncontrollable. As a consequence, a deterministic control loop has “blind spots” at the application layer, and the unpredictable delay of computing can destroy production links. With a view to ensuring the determinacy of cross-application closed-loop control at the application layer, this paper proposes an application-level deterministic system architecture that coordinates the service collaboration among industrial terminals, edge computing devices, and clouds. Furthermore, it develops an application-level deterministic mode applicable to various industrial scenarios and designs a decision-making mechanism involving management entities, overall decision-making, service types, task correlation diagrams, and strategic decision-making and translation.