The investigation of pyrolysis mechanisms in endothermic hydrocarbon fuels is crucial for optimizing the thermal management systems of supersonic aircraft. As a model compound, the effect of n-decane isomerization on the regulation of pyrolysis pathways and product distribution remains to be fully elucidated. In this work, reactive molecular dynamics (ReaxFF MD) simulations were employed to systematically study the influence of n-decane isomerization on its high-temperature pyrolysis behavior. Four n-decane isomers with different branching degrees were constructed, and their pyrolysis processes within the high temperature range were simulated. The reliability of the force field parameters was validated using quantum chemical calculations. Special emphasis was placed on analyzing the formation and consumption pathways of key products such as ethylene, methane, and hydrogen. The results demonstrate that isomerization reduces molecular symmetry and enhances the stability of central C-C bonds along the main chain, promoting bond cleavage toward terminal sites. Concurrently, it induces a noticeable shift in the product distribution from ethylene-dominated to methane-dominated profiles. Elevated temperatures significantly accelerate the pyrolysis rate, shorten the time required for complete fuel decomposition, and promote the formation of small molecule products. As an important intermediate, the peak concentration of ethylene decreases rapidly with increasing temperature, indicating that secondary reactions (e.g., dehydrogenation to acetylene and radical addition) play a critical role in modulating the final product distribution. The production of hydrogen increases markedly at high temperatures due to enhanced H-radical recombination reactions. Furthermore, coke precursors were detected across all high-temperature pyrolysis systems. This study reveals the underlying mechanisms through which n-decane isomerization influences pyrolysis pathways and product distribution at the atomic scale, providing theoretical support for the molecular design and thermochemical optimization of endothermic fuels.