A wavelength-dependent three-dimensional (3D) superlocalization imaging method on gold nanoislands (GNIs) chip was developed as a supersensitive single-molecule thyroid-stimulating hormone (TSH) nanobiosensor. Scattered and fluorescent signals from gold nanoislands on the substrate and quantum dots (QDs) nanoprobes were simultaneously isolated and acquired within an evanescent field layer generated by total internal reflection (TIR) of incident light using a dual-view device. The 3D TIR fluorescence images of TSH-bound QDs on the GNIs were obtained using z-axis optical sectioning at 10 nm intervals before/after immunoreaction to identify the optimal conditions for detection. The localized centroid position of QD nanoprobes and GNI were distinguished at a subdiffraction limit resolution using 3D Gaussian fitting to the point spread function. The QD TSH nanobiosensor using wavelength-dependent 3D TIR fluorescence-based single-molecule localization microscopy (3D TIRF-SLM) imaging technique showed an excellent detection limit of 90 yoctomoles (∼54 molecules) and a wide linear dynamic range of 1.14 zmol/L − 100 pmol/L for TSH. The detection sensitivity was about 4.4 × 109 times higher than conventional enzyme-linked immunosorbent assay and could successfully quantify TSH in human serum. The wavelength-dependent 3D TIRF-SLM technique may emerge as a reliable platform for ultrahigh-sensitive nanobiosensors at the single-molecule level and early diagnosis with quantification of disease-related ultra-trace biomolecules.