Understanding the structural evolution and bond-breaking behavior under cyclic loading is crucial for designing polymer nanocomposites (PNCs) with superior fatigue resistance. Coarse-grained models of PNCs filled with spherical carbon black nanoparticles (NPs) at varying filling fractions of φ were successfully constructed using molecular dynamics simulations. Structural and dynamic simulation results reveal that higher φ leads to increased aggregation of NPs and markedly restricts the relaxation behavior of the polymer matrix. Subsequently, fatigue testing of PNCs was conducted under low-strain cyclic tensile deformation, and the real-time bond-breaking behavior was tracked. The decay behavior of the bond number autocorrelation function was found to be accurately described by the KWW equation, enabling precise determination of the characteristic lifetime τf. With increasing φ, the dominant factor influencing bond-breaking behavior gradually shifts from the polymer network, including entanglements and cross-linking networks, to the filler network. This suggests the presence of a critical filling fraction φc where τf is maximized. For low-strain failure mechanisms, temperature field observations at varying cycles reveal that localized temperature rise emerges as the predominant factor. Furthermore, the mobility of both polymers and NPs increases with cycles. Specifically, the diffusion coefficient of polymer monomers shows a clear power-law relationship with the bond-breaking rate, characterized by . Finally, the stiffness of polymer chains significantly influences the fatigue behavior, evidenced by an initial increase followed by a decrease in the τf with increasing bending energy k. This behavior is attributed to the competitive relationship between high entanglement density at low k and enhanced preorientation at high k. In summary, this study provides a general paradigm for describing failure behavior under cyclic deformation and offers insights into fatigue mechanisms at the molecular level, thereby guiding the development of improved fatigue-resistant PNCs.