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To satisfy the needs of market customization, the traditional manufacturing is gradually transforming and upgrading into the intelligent manufacturing. In mass customization (MC), the assembly operations of modular products tend to be organized as the form of flexible mixed-model assembly line (FMMAL). The dynamic scheduling problem of FMMAL is quite complex with three issues of the product sequencing, station allocation and material delivery. At the same time, the disruption events of station failure, product inserting and product reworking are also considered. To solve this problem, a comprehensive framework combining the architecture of Internet of Manufacturing Things (IoMT) with the dynamic scheduling algorithms is proposed. Firstly, the IoMT-based FMMAL are constructed via the multi-agent system (MAS) and ubiquitous environment. Secondly, a mathematical model of FMMAL are formulated with the decision variables, optimization objectives and constraint conditions. Thirdly, the IoMT-oriented algorithms for dynamic scheduling are proposed including the fuzzy analytic hierarchy process (FAHP) for normalization, weighted sum of properties-improved genetic algorithm (WSP-IGA) for prescheduling, priority weights search-simulated annealing (PWS-SA) for rescheduling. Lastly, a discrete event simulation of a numerical case is conducted to demonstrate the practicality and validity of proposed theories and algorithms. The results show that the proposed hyper-heuristics (WSP-IGA and PWS-SA) can respectively realize the prescheduling and rescheduling of FMMAL in four modes including the synthesized mode, time-efficient mode, just-in-time mode and energy-saving mode, which are superior to the four referenced meta-heuristics.