The development of an aircraft industrial system is a complex process which faces the challenge of digital discontinuity in multidisciplinary engineering due to various interfaces between different digital tools, leading to extra development time and costs. This paper proposes an ontology-based system, aiming at functionality integration and design process automation, by Models for Manufacturing methodology principles. A tool-agnostic modelling, simulation and validation platform with Discrete Event Simulation and 3D simulation is enabled and demonstrated in a real case study. An ontology layer collecting the domain knowledge enables integration of the proposed system, accelerating the design process and enhancing design quality.