Quantum dots (QDs) are normally based on the semiconductor materials and widely used in biosensing, bioimaging, biolabeling, and biotreatment for their excellent properties. The ecotoxicity research of QDs correspondingly kept in rising in recent years. CdTe and CdTe/ZnS QDs were prepared via an improved process in aqueous phase, morphology of QDs was characterized with transmission electron microscopy, and optical properties were investigated via fluorescence spectrum. Ecotoxicity of CdTe and CdTe/ZnS were assayed by measuring the inhibitory growth of Rhodococcus sp. strain C1 when QDs existed in broth culture, which was screened from sewage, and its morphology was characterized with optical microscope and scanning electron microscope. CdTe QDs showed strong inhibitory effect against growth of Rhodococcus sp. strain C1, and little growth was observed after 72h cultivation. CdTe/ZnS QDs showed prophasic inhibition before 36h, and growth recovery was observed after 48h of cultivation. Enhanced optical properties and decreasing ecotoxicity were validated after ZnS shell formation, these results indicated that CdTe/ZnS QDs with core-shell structure has great potential in bio-applications.