Biological thiols play a critical role in biological processes and are involved in a variety of diseases. The discrimination detection of biological thiols is of increasing importance in clinical diagnosis. In this paper, a novel nanosensor was developed to discriminate cysteine (Cys) from homocysteine (Hcy) and glutathione (GSH) with multiple signals: colorimetric, photoluminescence (PL), and up-conversional photoluminescence (UCP). The nanosensor (NC-dots/AuNPs) was constructed by nitrogen-doped carbon dots (NC-dots) and gold nanoparticles (AuNPs) through assembling NC-dots "shell" on AuNPs and showed the obvious different response to Cys, Hcy, and GSH with colorimetric, PL, and UCP signals. The discrimination effect for Cys is originated from conformations and interaction difference of the thiols groups in Cys and Hcy and/or GSH with AuNPs. Among them, only Cys can quickly penetrate into the NC-dots "shell" of the composite and induce the dispersing of the aggregated NC-dots/AuNPs, which lead to the color change from purple to red and the recovery of PL and UCP of NC-dots. This assay was successfully applied for the detection of Cys in human serum with the detection limit of 4 nM.