CdTe QD-doped MIP-based TLC combined with a miniaturized fluorimeter system (namely the system) was developed to simultaneously detect malachite green (4-[(4-(dimethylamino)phenyl)(phenyl)methyl]-N,N-dimethylbenzenaminium chloride, MG) and crystal violet (4-(Bis{4-(dimethylamino)phenyl}methylidene)-N,N-dimethylcyclohexa-2,5-dien-1-iminium chloride, CV). The system integrated CdTe quantum dots-based molecularly imprinted polymers nanoparticles (CdTe-MIP/SiO2 NPs) with thin layer chromatography (TLC) plates. Firstly, CdTe-MIP/SiO2 NPs were synthesized by forming an imprinted layer on silica nanoparticle surfaces through a simple one-pot reaction. Then, the system was coupled with a miniaturized fluorimeter. Thus, the good optical properties of CdTe QDs (satisfactory fluorescence quantum yield, high fluorescence intensity, appropriate emission and excitation spectrums, good water solubility and photostability, tunability, etc.), specific recognition properties of MIPs toward template molecules and the related compounds, classical performances of TLC, and high sensitivity of the miniaturized fluorimeter were combined. The fluorescence intensity of the system exhibited linear quenching relationships with MG and CV concentrations within 0.01 similar to 1 mu mol/L and 1 similar to 20 mu mol/L, respectively. The detection limits for MG and CV were determined to be 8.5 nmol/L and 8.2 nmol/L, separately. Furthermore, the system successfully determined MG and CV in five kinds of fish samples within 10 min, with recoveries ranging from 91.9% to 114.6% for MG and 86.4% to 118.9% for CV. Validation by conventional HPLC showed that the system was suitable for the simultaneous determination of MG and CV. Therefore, the system is hopeful for extensive applications in real samples analysis.