As a necessary sulfhydryl amino acid, L-cysteine (L-Cys) maintains many physiological functions in the biological system. However, abnormal L-Cys levels can cause a variety of diseases. In our work, a highly sensitive and selective assay has been developed for sensing L-Cys using the morphological transformation of silver-based materials induced by Cr3+. In this sensing system, Cr3+ could etch the silver nanoflakes into silver nanoparticles, accompanied by a change in absorbance, which decreases at 395 nm, creates a new peak at 538 nm, and keeps increasing the absorbance with the addition of Cr3+ concentration. Meanwhile, under the naked eye, the solution color changes from bright yellow to dark purple. Because of the strong affinity between L-Cys and Cr3+, L-Cys could inhibit the induction of Cr3+ on silver-based materials, thereby preventing changes in the configuration, absorption spectrum, and color of silver-based materials. Taking advantage of this point, we can quantitatively detect the concentration of L-Cys. A linear relationship between the absorbance ratio (A538 nm/A395 nm) and L-Cys concentration was found in the range of 0.1–0.9 μM, and the detection limit was 41.2 nM. The strategy was applied to measure L-Cys spiked in beer and urine samples, with recovery from 93.80 to 104.03% and 93.33% to 107.14% and RSD from 0.89 to 2.40% and 1.80% to 6.78%, respectively. This detection strategy demonstrates excellent selectivity and sensitivity, which makes it a practical and effective method for the detection of L-Cys in real samples.