For the first time, we report a simple method to fabricate a quantum dot (QD)-polymer composite completely via aqueous media from synthesis of QDs to formation of composite. A series of L-cysteine-capped CdTe QDs with tunable emission from green to red were prepared by using hydrothermal techniques, and the corresponding average particle sizes were estimated to be from 2.5 to 4.1 nm. After incorporating these CdTe QDs into the waterborne polyurethane (WPU) prepolymer aqueous suspension, we obtained a transparent nanocomposite film by casting and evaporating. The optical properties of the aqueous CdTe QDs solution and CdTe-WPU composites were investigated by UV-vis absorption and photoluminescence (PL). The results indicate that the quantum yield (QY) and the photochemical stability of the CdTe QDs in both CdTe-WPU aqueous complex and solid composite are enhanced significantly, because of a thicker and more compact passivating layer formed on the surface of CdTe QDs via the reaction between the groups of -NCO and -NH2. In addition, the transmission electron microscopy (TEM) and laser scanning confocal fluorescence microscopy (LSCFM) images show that the CdTe QDs with excellent crystalline structure and strong florescence emission are well-dispersed in the WPU matrix without obvious aggregation or agglomeration. On the basis of the versatile properties of WPU and the photoluminescence originating from the CdTe QDs, these new fluorescent composite materials could have great potential applications. This approach provides a simple route for preparation of various fluorescent QD-polymer composite materials from aqueous QD solutions with neither ligand exchange nor phase transfer.