Personalised production allows the supply chain (SC) to exist in various dynamic fluctuations within a make-to-order (MTO) environment. An SC for personalised production has redundant inventory and operation capacity; therefore, it requires a system that can achieve recoverability for operation resilience. Thus, a standalone cyber physical system (CPS) has limitation for SC control with MTO. To solve this problem, the CPS must be coordinated, and a systematic approach is required. This study proposes a cyber physical logistics system (CPLS) that is coordinated with the agent cyber physical production systems in a multi-level CPS structure. This multi-level architectural framework is designed to provide technical functionalities for resilient SC control. The service composition procedures of technical functionalities on the distributed digital twin (DT) simulation are divided into type and instance stages. The operation procedures of the DT application and technical functionality of the DT engine are suggested. The proposed CPLS has appropriate service composition and operation for the bullwhip and ripple effects, which are the two main SC-related problems. This study illustrates an early case of CPLS that can minimise differences among assets using distributed DT simulation; furthermore, the study establishes an SC and production plan based on the DT simulation results.