Developing type-II heterostructures with a spatial separation of photoexcited electrons and holes is a useful route to promote photocatalytic hydrogen generation. However, few investigations on the charge transfer process across the heterojunction have been carried out, which can allow us to uncover the reaction mechanism. Herein, CdSe quantum dots (QDs) and TiO2 nanocrystals were synthesized and combined in water yielding CdSe/TiO2 type II heterostructures. It was found that mercaptopropionic acid as bifunctional molecules could bind with CdSe and TiO2 to form a cross-linked morphology. The charge carrier dynamics of bare CdSe and CdSe/TiO2 were detected using femtosecond transient absorption spectroscopy. In the presence of TiO2, the average exciton lifetime of CdSe QDs was apparently decreased, owing to the electron transfer from photoexcited CdSe to TiO2. Particularly, the electron-transfer rate from small CdSe QDs (3.0 nm) was much faster than that from big CdSe QDs (4.2 nm). The improved photocatalytic hydrogen generation was observed for CdSe/TiO2 compared to bare CdSe QDs. The enhancement factor for small CdSe QDs was higher than that for big CdSe QDs, which was in good agreement with the electron-transfer rates. This result indicated that the electron transfer between CdSe and TiO2 played an important role in photocatalytic hydrogen generation on CdSe/TiO2 type-II heterostructure. Our study provides a fundamental guidance to construct efficient heterostructured photocatalysts by delicate control of the band alignment.