This paper presents the sharing of our experiences and lessons learned to modernize a warship with C6ISR utilizing the digital engineering MBSE models of complex systems. We captured Enterprise Architecture (EA) DoDAF views, KPP and KSA in Capability Views (CV). At the EA, information passes into domain specific SoS Block Definition Diagrams (BDD) and Internal Block Diagrams (IBD) to interface and exchange information via SysML models and generate the Interface Control Document (ICD) automatically. The paper illustrates the mapping of EA with SoS digital models and tracing from EA to SoS MOE, MOP, MOS and TPM. The paper applies a Use Case to exemplify OOSEM life cycle activities for requirements traceability. The paper has demonstrated that both EA and SoS are derived from Systems Engineering (SE) process and can be validated and verified via the “V‐Model” and endorse the noticeable reduction in the total development cost per complex systems project.