With the development of global economy, supply chain, as a recognised complex system, is becoming more complex for analysis. In this context, it is worth introducing the perspective of complex system in perceiving and modelling of supply chain system to address its dynamic, stochastic and uncertain characteristics. Therefore, this paper proposes a methodological framework of supply chain modelling and simulation based on the fractal perspective, and presents an all-round and systematic exposition of concept modelling and distributed simulation by means of multi-agent technology. In this framework, different supply chain scenarios focusing on manufacturing, inventory and transportation can be easily modelled and simulated at different scales and levels. In addition, a prototype system which implements the methodological framework and the key implementation techniques are presented as well. Finally, a supply chain example, which supposes manufacturer as the core member, is modelled and simulated with the prototype system to illustrate the effectiveness of the proposed framework.