The petrochemical industry belongs to the dangerous chemical industry. The optimization of supply chain can significantly improve the overall profits of enterprises, reducing costs and risks. Based on the value-at-risk theory, this paper proposes an optimal dispatching model for chemical fuel supply chain, which is used to solve the uncertainty of market demand and capacity scale. The sample mean estimation method is used to calculate the optimal demand risk threshold and capacity risk threshold. The calculation results show that the higher the risk threshold is, the lower the supply chain cost will be. The impact of chemical fuel market demand risk threshold on the supply chain object function is greater than that of capacity risk threshold on the supply chain object function. Therefore, the supply chain optimal dispatching should take the market demand as a priority. According to calculation results, the optimal values of demand risk threshold and capacity risk threshold are set to 0.26 and 0.1, respectively. This research can provide theoretical reference for the large-scale supply chain optimal dispatching under the condition of uncertain factors.