Abstract-Software Product Line Engineering (SPLE) has drawn large amounts of attention during the last two decades as it offers the benefits of reducing cost and time to market by reusing requirements and components. Recently, more and more large scale industries start to implement SPLE in their domains (combining SPLE with model-based modelling methods). However, the problem of how to combine SPLE with ModelBased System Engineering is still a challenge, as systems are much broader than the software domain. Unlike software engineering, system engineering has to consider the physical resources aspect. This paper classifies typical types of physical variability and provides general modelling solutions for each type of physical variation at the system design stage. Specifically, this approach combines a variability model with a SysML Block Definition Diagram and an Internal Block Diagram to model the contextual variability, architectural variability, connector variability, instance number variability, component variability, location variability and evolutional variability of physical designs. Variability is modelled separately to help reduce the complexity of design models. Last but not least, the proposed method is illustrated by an aircraft system case study.