Malachite green has good bactericidal properties, which can effectively prolong the life of fish with scale damage during transportation. Although the State prohibits the use of malachite green in aquatic products, it is still on sale in the market. Using malachite green as template, molecularly imprinted silica coated CdTe quantum dots were prepared. As there is a good linear relationship between malachite green concentrations and the variety of fluorescence intensity of CdTe quantum dots, a quenching method could be used to quantitative analysis of malachite green, of which linear range was 0.89-4.83 μmol/L, and the lowest detection limit is 0.03867 μmol/L. This method has good selectivity and lays an experimental foundation for the development of new fluorescent sensors.