Understanding, modeling, and reducing the cycle-to-cycle variability (CCV) of combustion in internal combustion engines (ICE) is a critical challenge to design engines of high efficiency and low emissions. A high level of CCV may contribute to partial burn, misfire, and knock in extreme engine cycles, which affects engine performance and eventually damages the engine. The origins of CCV have been studied both experimentally and numerically, and the variability of in-cylinder aerodynamics is recognized as one of the most important sources of CCV. However, a detailed and quantitative explanation of how in-cylinder flow CCV is generated is not yet clear. The objective of the present study is to develop a methodology to localize inside the chamber of a spark-ignition engine (SIE) the origins of flow variabilities and to identify some driving mechanisms leading to combustion variabilities. Multi-cycle wall-modeled large-eddy simulations (LES) for the TU Darmstadt optical engine under fired conditions are performed using the CFD solver Converge 3.0. The evolution of organized large-scale structures and the small-scale turbulence of the in-cylinder flow are analyzed using a developed methodology that includes the empirical mode decomposition (EMD) method adapted for 2D and 3D flow fields, and a vortex identification tool Γ3p. The contributions of different parts of the flow to CCV are quantified. In Part I of this work, the LES framework is validated against experimental data, and CCV of large-scale structures is characterized at spark timing. In Part II, the overall flow development during compression and intake strokes are quantitatively analyzed, and links are built between different engine phases to establish the cause-and-effect chain. Other CCV factors, such as spray injection and exhaust gas recirculation, are not included in the current study. However, the developed methodology for in-cylinder flow analysis could be used in studies on other engine configurations to improve the development of engine designs.Novelty and significance statementIn this work, the cycle-to-cycle variability (CCV) of combustion in a spark ignition engine is investigated to give a deeper understanding of CCV generation. The present study focuses on CCV caused by the stochastic nature of internal turbulent flow structures. LES approach is chosen due to its ability to capture CCV. The LES methodology was validated in a motored case in Ding et al. (2023). In the present study, it is validated in a reactive case against experimental in-cylinder pressures and velocity fields.A first novelty is the application of EMD methods combined with topology-based techniques to reactive LES results to characterize flow structures of different scales in the three-dimensional domain and to quantify separately their impacts on combustion.A second novelty and important finding is that a link is established between the combustion speed and the tumble formation and destabilization near BDC.Throughout our analyses in Part I and II, starting from the spark-ignition timing and going back to the early intake phase, a cause-and-effect chain is finally established between the development of in-cylinder flow and the combustion variability.