The current state of the practice of Model‐Based Systems Engineering (MBSE) methodologies, system specification models, and executable system simulations lack the capability of simulation execution within a single system specification model with the fidelity required for time‐dependent simulation towards the design, analysis, and optimization of complex software‐based systems. In this paper we develop and demonstrate a modular simulation‐based MBSE approach capable of filling this gap. To accomplish this within a single system specification model we embed a combination of modeled simulation activities, opaque behaviors, and simulation specific functions to execute and manage the time‐dependent simulation variable arrays. We applied our MBSE approach on the design and analysis of a hybrid on‐prem/cloud data system example that meets the complex, software‐based, and time‐dependent requirements this approach was built to solve. The results show that our approach produces a modular and time‐dependent simulation‐enabled system specification model that accurately estimates cloud‐based system performance and storage cost as a function of time. Emergent system behaviors observed from the simulation results indicate the system model provides foundational design and analysis capabilities that are required for applying system optimization algorithms.