We developed highly luminescent and cost-effective quantum dot (QD)-neutravidin (NTV) bioconjugates to detect the tyrosine kinase B (TrkB) receptors distributed in the cultured hippocampus neurons. Hippocampal neurons were incubated with biotinylated anti-TrkB antibody, followed by further incubation with QD-NTV bioconjugates. QD-NTV biomarkers on the extracellular domain of TrkB receptors were imaged by the combined atomic force microscope and confocal laser scanning microscope (AFM-CLSM) providing resolved (nanometer-scale) structural and fluorescent images. We found that TrkB receptors were distributed over the neuronal cell bodies (soma) and neurites. TrkB receptors in the somata looked more concentrated, but those in the neurites appeared punctate. Thus, our QD-based immunocytochemistry technique combined with an AFM-CLSM can be used for three-dimensional morphology of neurons on nanometer-scale structural resolution and their fluorescence images with QDs. Furthermore, this technique can be applied for real-time fluorescence imaging or long-term study of live neurons.