In today's world, the Industries are focusing on digitalized transformation as an Industry revolution 4.0 which encompassing numerous innovations and creating new market dynamics. Incorporating innovative systems like drone transportation systems and their flexibility is currently the main concern for the companies on the shop floor. It allows the manufacturing stations to transport the product from one station to another. However, the adoption of such a system requires the development of integrated approaches that should consider all interfacing problems between the different components of the global production system. The main aim of the work is to analyze the potential use of autonomous drones, mobile robots, and production systems collaborate together in different Scenarios in a given manufacturing system. Concretely, a Model-based system Engineering (MBSE) approach is carried out to model the integrated production and transportation systems at the black-box level. And identifies their functionality and exchanged flow between the subsystems in physical and Cyber components levels. The presented work provides the first step in developing the complete heterogeneous solution within the industry 4.0 Smart factory paradigm. The Laboratory of digital science of Nantes (LS2N)-Smart factory is the supporting use case for this research work.