Despite numerous studies that consider service level, reliability, robustness, and resilience rates of individual factories in a supply chain system (SCS), the interactions among connected factories and the impact of those interactions on overall supply chain reliability, robustness, and resilience have been rarely studied. Moreover, ensuring the reliability, robustness, and resilience while considering uncertainties induced by various sources, such as transportation delay and manufacturing process variability, in individual factories and routes is a highly complex task. An extensive review of the current literature on global SCS design and analysis shows an urgent need to understand the concept of factory-to-factory supply chain systems, and to develop methods and techniques to efficiently measure and design them. Thus, this research addresses different imperative needs for SCSs, which have been structured into six research thrusts: (1) measurement of SCS service level (SL), (2) assurance of system SL robustness in complex supply chain networks (SCNs), (3) cost-efficient robust global SCS design under uncertainty, (4) measurement and optimization of reliability in complex SCSs, (5) measurement of resilience of multi-level SCSs, and (6) measurement and analysis of reliability, resiliency, and robustness of SCSs.