Hybrid systems (HSs) of functional organic ligands and colloidal quantum dots (QDs) exhibit unique physical properties that do not emerge in QDs themselves owing to a synergetic effect and are expected to be applied to luminescence switching and photoenergy conversion materials. However, HSs have two inherent issues. The high surface-to-volume ratio of QDs makes them prone to generating trap states during the hybridization process, resulting in a performance decline of the HSs. The second issue is that the number of attached ligands on a single QD is distributed. The observed properties represent the average ensemble of these compositions, making it difficult to extract elementary processes. In this study, we employed Z-type ligand exchange and analyzed the energy transfer process using a stochastic model to address these challenges. The luminescence quantum yield of diarylethene derivative (DAE)-CdSe/CdS HSs, formed through Z-type ligand exchange, remained nearly constant compared to that of the as-prepared CdSe/CdS QDs without additional formation of trap states. We elucidated the energy transfer processes from excited CdSe/CdS QDs to closed-form DAE (c-DAE) using a stochastic model, enabling us to estimate the rate constant of energy transfer from a single QD to a single c-DAE and the mean number of c-DAE as a function of UV irradiation time. The distance from the QD to c-DAE calculated from the energy transfer rate is in good agreement with the estimated value from the QD diameter and adsorbed c-DAE length. In addition, we found that the trap states on the surface of the QDs were reversibly formed by the photochromic reaction, and the number of trap states linearly increased with UV irradiation time. This methodology has the potential to be extended to other QDs and functional organic ligand combinations, offering more accurate understanding of the structural analysis and elementary exciton processes of HSs.