Logistics interfaces with manufacturing throughout the entire production process need synchronous operations. For achieving integrated organization and operations between manufacturing and logistics, this article introduces the concept of shop-floor logistics and manufacturing synchronization with four principles, including: 1) synchronization-oriented manufacturing system; 2) synchronized information sharing; 3) synchronized decision making; and 4) synchronized operations. The marriage of the principles rendered the development of an overall framework of the Industrial Internet of Things (IIoT) and digital twin-enabled graduation intelligent manufacturing system (GiMS). A mixed-integer programming-based synchronization mechanism is proposed under GiMS. To meet the requirement of fast decision making in real-life shop-floor logistics and manufacturing synchronization problems, an equivalent constraint programming model is developed and tested. The observation and analysis of the case company show the advantage of the proposed concept and approach with the best performance regarding key performance indicators. The concept of synchronization provides an insight for understanding the interaction of logistics and manufacturing at the operational level. This article potentially enables manufacturers to reevaluate and develop their manufacturing planning and control strategies in the IIoT and digital twin-based manufacturing environment.