Roxarsone (ROX) as an organoarsenic feed additive has been widely used in livestock breeding and poultry industry, but ROX can degrade into highly toxic inorganic arsenic species in natural environments to threaten to the environment and human health. Therefore, there is a considerable interest in developing convenient, selective and sensitive methods for the detection of ROX in livestock breeding and poultry industry. In this work, a fluorescent molecularly imprinted polymer (MIPs) probe based on amino-modified Mn-ZnS quantum dots (QDs) has been developed by sol–gel polymerization for specific recognition of ROX. The synthesized MIPs-coated Mn-ZnS QDs (MIPs@Mn-ZnS QDs) have highly selective recognition sites to ROX because there are multi-interactions among the template ROX, functional monomer phenyltrimethoxysilane and the amino-functionalized QDs such as the π–π conjugating effect, hydrogen bonds. Under the optimal conditions, an obvious fluorescence quenching was observed when ROX was added to the solution, and the quenching mechanism could be explained as the photo-induced electron transfer. The MIPs@Mn-ZnS QDs sensor exhibited sensitive response to ROX in the linear range from 3.75 × 10−8 M to 6.25 × 10−7 M (R2 = 0.9985) and the limit of detection down to 4.34 nM. Moreover, the fluorescence probe has been applied to the quantitative detection of ROX in feed samples, and the recovery was in the range of 91.9% to 108.0%. The work demonstrated that the prepared MIPs@Mn-ZnS QDs probe has a good potential for rapid and sensitive determination of ROX in complicated samples.