In addition to the long‐term goal of mitigating climate change, the current geopolitical upheavals heighten the urgency to transform Europe's energy system. This involves expanding renewable energies while managing intermittent electricity generation. Hydrogen is a promising solution to balance generation and demand, simultaneously decarbonizing complex applications. To model the energy system's transformation, the project TransHyDE‐Sys, funded by the German Federal Ministry of Education and Research, takes an integrated approach beyond traditional energy system analysis, incorporating a diverse range of more detailed methods and tools. Herein, TransHyDE‐Sys is situated within the recent policy discussion. It addresses the requirements for energy system modeling to gain insights into transforming the European hydrogen and energy infrastructure. It identifies knowledge gaps in the existing literature on hydrogen infrastructure‐oriented energy system modeling and presents the research approach of TransHyDE‐Sys. TransHyDE‐Sys analyzes the development of hydrogen and energy infrastructures from “the system” and “the stakeholder” perspectives. The integrated modeling landscape captures temporal and spatial interactions among hydrogen, electricity, and natural gas infrastructure, providing comprehensive insights for systemic infrastructure planning. This allows a more accurate representation of the energy system's dynamics and aids in decision‐making for achieving sustainable and efficient hydrogen network development integration.