Companies with manufacturing systems that are more responsive and resilient will be able to survive or even gain market shares in the face of the unpredicted variable of an outbreak similar to the COVID-19 pandemic. Motivated by an industrial company restructuring its manufacturing system with the layout of fixed-position assembly islands (FPAI) during the COVID-19 pandemic, this paper introduces the synchronization-oriented reconfiguration of FPAI under Graduation Intelligent Manufacturing System (GiMS). Inspired by the graduation ceremony, a novel manufacturing mode-Graduation Manufacturing System (GMS) with ticket-based reconfigurable structures, is designed for organizing production operations with simplicity and resilience for the layout of FPAI. The IIoT and digital twin-enabled GiMS is developed for transforming real-time visibility in operations to support the reconfiguration of the manufacturing system. A synchronization-oriented reconfiguration mechanism is proposed to achieve the synchronous interaction among changing customer demand, island configuration, and production activities allocation rapidly and cost-effectively. Cloud services integrating the proposed reconfiguration mechanism are developed for managers and onsite operators for supporting the successful reconfiguration implementation with enhanced operational visibility. Through the case study of an industrial company, the effectiveness of the proposed concept and approach is verified.