Addressing climate change requires a significant reduction in greenhouse gas emissions, with optimizing existing technologies offering a promising solution. In gasoline engines, the occurrence of knocking combustion presents a major obstacle to enhancing efficiency. Here, the engine process exhibits cycle-to-cycle variations, which affect the combustion process and consequently alter the boundary conditions for knocking combustion initiation. The statistical nature of these variations poses a research challenge, requiring specialized methods and analytical approaches. While previous studies have identified correlations between flow characteristics and the combustion process, whether these correlations can be extended to the initiation of knocking combustion remains unresolved and is addressed here. In this study, measurements of knocking combustion of a surrogate fuel in a single-cylinder research engine are used as the basis for a subsequent multi-cycle LES study. Here, the knocking combustion initiation is predicted employing a recently developed precursor model. The LES results are validated against the experimental data in terms of averaged combustion and knock quantities, taking into account cycle-to-cycle variations. In particular, it is shown that the simulations can predict the probability of knocking combustion initiation locations in the cylinder in agreement with the experiment. The validated simulation data is then used for investigation of the cause-and-effect chain of knocking combustion initiation. Here, the relationships among flow structures, flame propagation and the auto-ignition process are analyzed qualitatively and quantitatively. Notably, large-scale flow structures are found to affect early flame propagation, which in turn influences the overall combustion process. Furthermore, differences in the local early flame propagation are found to determine the local and global auto-ignition process. In summary, this study advances the understanding of knocking combustion initiation by unraveling the complex relationships among flow structures, flame propagation, and auto-ignition processes, providing valuable insights into the cause-and-effect chain of knocking combustion initiation.