The histidine/Mn3O4/CdTe quantum dots (HMQ) composites with good magnetic resonance/fluorescent imaging and absorbance performance have been prepared based on biomimetic mineralization method, on which the peptide served as a carrier to guide the formation of Mn3O4 and CdTe quantum dots. The fluorescence of HMQ could be quenched by malachite green (MG), whereas the magnetic resonance signal (T1-MRI) was enhanced. Also, there is a linear correlation between the concentrations of MG added and the decreasing fluorescence intensity of HMQ (F0/F), the detection range is 0.06851–1.096 nmol l−1, and the LOD is 0.02750 nmol l−1. The corresponding T1WI detection range is 13.7–95.9 nmol l−1, and the LOD is 7.617 nmol l−1. Furthermore, the fluorescence quenching spectra of the HMQ adopted by MG have been analyzed, of which the data fit well with the law of pseudo-second-order kinetics, indicating that the prepared HMQ has good absorption properties. Therefore, HMQ could be used as an MRI/fluorescent dual sensor for the detection of MG.