Modelling and analysis of complex and co-ordinated supply chains is a crucial task due to its inherent complexity and uncertainty. Therefore, the current research direction is to devise an efficient modelling technique that maps the dynamics of a real life supply chain and assists industrial practitioners in evaluating and comparing their network with other competing networks. Here an effective modelling technique, the hybrid Petri-net, is proposed to efficiently handle the dynamic behaviour of the supply chain. This modelling methodology embeds two enticing features, i.e. cost and batch sizes, in deterministic and stochastic Petri-net for the modelling and performance evaluation of supply chain networks. The model is subsequently used for risk management to investigate the issues of supply chain vulnerability and risk that has become a major research subject in recent years. In the test bed, a simple productive supply chain and an industrial supply chain are modelled with fundamental inventory replenishment policy. Subsequently, its performance is evaluated along with the identification and assessment of risk factors using analytical and simulation techniques respectively. Thus, this paper presents a complete package for industrial practitioners to model, evaluate performance and manage risky events in a supply chain.