Supply chain systems are hybrid dynamic systems composed of continuous elements such as supply, production, distribution performed by supplier, manufacturer, distributor, discrete element such as transportation, demand performed by logistics company, consumer. Traditional method of modeling supply chain looking supply chain as discrete event system or continuous time system canpsilat reflect dynamic character or random character. A hybrid Petri nets model of supply chain is developed with a discrete-continuous combined modeling approach in this paper. Global conflicts are solved by solving multi-object programming model. Local conflicts are solved by setting fixed rate and local priority. Through solving optimal firing speed of continuous transitions in hybrid Petri nets model, optimal capacity combination is obtained under the uncertainty condition of consumer demand, waster rate of production and transportation disruption.