Rapid and on-site qualitative and quantitative analysis of small molecules (including bioflavonoids) in biofluids are of great importance in biomedical applications. Herein, we have developed two deep learning models based on the 3D fluorescence spectra of gold nanoclusters as a single probe for rapid qualitative and quantitative analysis of eight bioflavonoids in serum. The results proved the efficiency and stability of the random forest-bidirectional long short-term memory (RF-BLSTM) model, which was used only with the most important features after deleting the unimportant features that might hinder the performance of the model in identifying the selected bioflavonoids in serum at very low concentrations. The optimized model achieves excellent overall accuracy (98-100%) in the qualitative analysis of the selected bioflavonoids. Next, the optimized model was transferred to quantify the selected bioflavonoids in serum at nanoscale concentrations. The transferred model achieved excellent accuracy, and the overall determination coefficient (R2) value range was 99-100%. Furthermore, the optimized model achieved excellent accuracies in other applications, including multiplex detection in serum and model applicability in urine. Also, LOD in serum at nanoscale concentration was considered. Therefore, this approach opens the window for qualitative and quantitative analysis of small molecules in biofluids at nanoscale concentrations, which may help in the rapid inclusion of sensor arrays in biomedical and other applications.