We report an all-aqueous synthesis of highly photoluminescent and stable ZnS quantum clots (QDs) with water as the medium. The method involves first synthesizing ZnS QDs with 3-mercaptopropionic acid (MPA) as the capping molecule and then replacing some of the MPA with (3-mercaptopropyl)trimethoxysilane (MPS). The resultant MPS-replaced ZnS QDs were about 5 nm in size with a cubic zinc blende crystalline structure, and they had both MPA and MPS on the surface as confirmed by Fourier transform infrared (FTIR) spectroscopy. They exhibited blue trap-state emissions around 415 nm and a quantum yield (QY) of 75% with rhodamine 101 as the reference, and they remained stable for more than 60 days under ambient conditions. Through the capping-molecule replacement procedure, the MPS-replaced ZnS QDs avoided the shortcomings of both MPA/ZnS QDs and MPS/ZnS QDs and acquired the advantages of strong photoluminescence and good stability, which are important to QD applications, especially for bioimaging.