The initial and subsequent surface reaction mechanisms of 1,3-cyclohexadiene on the Si(100)-2x1 surface were theoretically explored, focusing on the possible first-neighbor interactions. Five different initial reaction channels leading to nine different surface products were identified, confirming previous experimental reports of inter-dimer structures. Among the nine identified products, five of these surface products are new species that have not previously been reported. Potential energy surface studies reveal that the net reaction barriers within a given channel are very small, indicating that the final product distributions within that channel are determined by thermodynamics. On the other hand, thermal isomerizations between different channels are not expected to occur easily. Therefore, the surface product distributions among the five different channels are more likely to be determined by kinetics. As a result, understanding the relationships among the available reaction channels both kinetically and thermodynamically is essential for properly interpreting the experimental results. The current study shows that the subsequent surface chemical reactions of unsaturated initial surface products are strongly coupled with the first-neighbor interactions.