Acknowledging recent breakthroughs in the context of deep bio-inspired neural networks, several architectural deep network options have been deployed to create intelligent systems. The foundations of convolutional neural networks are influenced by hierarchical processing in the visual cortex. The graph neural networks mimic the communication of biological neurons. Considering these two computation methods, a novel deep ensemble network is used to propose a bio-inspired deep graph network for creating an intelligent supply chain model. An automated smart supply chain helps to create a more agile, resilient and sustainable system. Improving the sustainability of the network plays a key role in the efficiency of the supply chain’s performance. The proposed bio-inspired Chebyshev ensemble graph network (Ch-EGN) is hybrid learning for creating an intelligent supply chain. The functionality of the proposed deep network is assessed on two different databases including SupplyGraph and DataCo for risk administration, enhancing supply chain sustainability, identifying hidden risks and increasing the supply chain’s transparency. An average accuracy of 98.95% is obtained using the proposed network for automatic delivery status prediction. The performance metrics regarding multi-class categorization scenarios of the intelligent supply chain confirm the efficiency of the proposed bio-inspired approach for sustainability and risk management.