Highly diverse factors including technological advancements, uncertain global market and mass personalisation are believed to be main causes of ever-growing complexity of manufacturing systems. Although complex systems may be needed to achieve global manufacturing requirements, complexity affects on various factors, such as: system development effort and cost, ease of re-configuration, level of skill required across the system life-cycle (e.g. design, operate and maintain). This article aims to develop a scientifically valid and industrially applicable complexity assessment approach to support early life-cycle phases of component-based automation systems against unwanted implications of structural system complexity. The presented approach defines component-based automation system as a constellation of basic components which can be represented in various design domains, such as: mechanical, electrical, pneumatic, control, etc. Accordingly, structural complexity is expressed as the combination of both inherent complexity of system entities and topological complexity resulting from the integration of elements of such constellations in a multi-layered network. The proposed approach is used to specify and implement a complexity assessment module which can be integrated into a series of virtual system design software solutions, in order to add complexity assessment as part of the design support and validation tools used by manufacturing engineers. Consequently, the proposed approach is integrated into the vueOne virtual engineering tool, wherein virtual automation system design data can be streamlined and used as input to the theoretical complexity model. In the developed tool, only mechanical and logical design domains are considered due to the limited data availability in early design phase. Inherent complexity of both mechanical and logical system entities and their interactions are expressed as a function of domain-specific design elements, and topological complexity is defined as the graph energy of the corresponding design connectivity matrix. Furthermore, the values of mathematical model parameters are determined based on an optimisation study, where subjective opinions of system/control engineers regarding the effort/difficulty associated with the development of thirty different component-based automation system designs are correlated with the corresponding complexity model outputs to minimise the prediction errors. The proposed approach is also demonstrated on a modular production system consisting of four sub-modules. The study shows that the approach can help designers/managers to better identify root causes of structural system complexity, and provides a systemic approach to compare alternate system designs during early system planning phase.