Due to the intensely increasing competition and rapidly changing demand, Mass Customization(MC) manufacture has been the new trend for modern enterprises to respond quickly to the variational and individual demand in global market. To satisfy the operation of MC manufacture, its supply chain must be effective and flexible enough. Findings of researches and practices have shown that some intelligent activities, such as negotiation, decision and collaboration, have become the “bottleneck” to improve the performance of supply chain. This paper applied the Autonomous Intelligent System(AIS) to deal with the intelligent activities intelligently and automatically, and thereof provided a new method for the Supply Chain Management(SCM) on MC manufacture. First, a new supply chain model based on E-HUB was presented according to the requirements of MC manufacture, and then the structure and operation of AIS were designed to support that SCM. Finally, the development technology of AIS was discussed.