Integrated Modular Avionics (IMA) architecture host multiple federated avionics applications into a single platform and provides benefits in terms of Size, Weight and Power (SWaP), nonetheless brings a high level of complexity to aircraft control systems. The thesis presents Model-Based System Engineering a novel, structured development methodology to cope efficiently with increased complexity due to IMA. Using ARCADIA methodology and the open source Capella tool, the developed methodology is implemented for a complete design cycle: starting with capturing requirements from the aircraft level to streamlining the development, integration of avionics application in an ARINC 653 platform. The proposed methodology provides effective traceability and management of specification artifacts from aircraft to system to item-level adhering to SAE ARP4754A guideline. Further, the thesis presents the capability of the MBSE framework to effectively address a few technological variants through the proposed methodology. To illustrate the efficiency of the methodology and MBSE approach an Environmental Control System (ECS) case study is presented. The case study focuses on implementing ECS in an IMA architecture using MBSE framework and proposed methodology. However, the derived methodology is also applicable to other systems. Further, the case study also presents a demonstration of integrating Cabin Pressure Control Sub-system (CPCS) into a real-time IMA platform for validation of MBSE approach. In addition, the thesis provides important insights in challenges and advantages of the MBSE process in contrast to the traditional paper-based specification process.