The article discusses the challenges faced in green hydrogen generation using PEM electrolysis cells due to fluctuations in renewable energy inputs and degradation rates impacting performance. A bond graph model-based power loss tracking approach is proposed to analyze the effects of degradation on PEM electrolysis cell performance. This approach enables real-time tracking of power losses at various levels, providing valuable insights into system dynamics and degradation impact. The model, implemented in 20-Sim software, generates governing equations automatically, facilitating usability. A sensitivity analysis showcases the model's responsiveness to parameter changes. The simulation-based validation within a green hydrogen production platform confirms the model's capabilities, supporting diagnostics and prognostics of PEM electrolysis cells. The article emphasizes the importance of efficiency tracking for maximizing performance and durability of PEM stacks, aiding in material selection and fault detection. By estimating power losses, the model helps in making informed design decisions for more efficient green hydrogen production.