The possible reaction mechanisms for the experimentally observed hydrogen transfer between the herbicide cycloxydim (CD) and the triplet fungicide chlorothalonil (CT) were identified with density functional theory (DFT) and time-dependent density function theory (TDDFT) computations. Excited energy transfer (EET) calculations indicate that reactants for intermolecular hydrogen transfer were formed via energy transfer from triplet CT to ground state CD. Three possible reaction pathways after EET were identified, and hydrogen transfer from the hydroxyl group on the cyclohexane ring of CD to CT exhibited the lowest energy barrier. Natural population analysis (NPA) along the reaction pathways has confirmed that the pathways involved either electron transfer induced proton transfer or coupled electron–proton transfer, leading to different potential energy profiles. Electrostatic potential (ESP) study substantiated the reaction mechanisms in different pathways. This study suggests an explanation for the accelerated photodegradation of CD by CT and provides a pipeline for future studies of photoinduced intermolecular hydrogen transfer.