Knocking combustion is the main bottleneck when downsizing and supercharging spark-ignition engines for pursuing higher thermal efficiency. The effects of thermodynamic conditions and thermal and/or fuel stratifications have been extensively studied, but the role of fuel properties in knocking evolutions has not been fully clarified. In this study, the synchronization measurement on knocking combustion through simultaneous pressure acquisition and high-speed direct photography was performed on an optical rapid compression machine. The knocking characteristics of isooctane and methane were investigated comparatively under different initial conditions and thermal boundary conditions. Meanwhile, the correlations of pressure oscillations, flame propagation, end-gas autoignition, and gas dynamics were discussed and compared between different fuels. The results show that for isooctane at given intake temperatures, end-gas autoignition timing is advanced and knocking intensity is enhanced significantly as intake pressure is increased, but the end-gas autoignition does not result in pressure oscillations in methane scenarios. With thermal boundary conditions being considered, the autoignition timing is advanced at higher wall temperatures for both fuels. However, isooctane scenarios are featured by prevalent secondary autoignition and stronger knocking intensity, whereas methane scenarios always exhibit end-gas autoignition behavior without obvious pressure oscillations. These distinctions are clearly manifested in the evolutions of autoignition reaction wave propagation. Furthermore, the correlation between knocking intensity and energy density indicates that the underlying reasons are ascribed to the higher chemical reactivity for isooctane than that for methane fuel. The current work shall provide insights into combustion control and knocking suppression using the collaborative optimization of engine operations and fuel interactions.