Cystine-enriched food supplements are increasingly popular due to their beneficial health effects. However, the lack of industry standards and market regulations resulted in quality issues with cystine food products, including cases of food adulteration and fraud. This study established a reliable and practical method for determining cystine in food supplements and additives using quantitative NMR (qNMR). With the optimized testing solvent, acquisition time, and relaxation delay, the method exhibited higher sensitivity, precision, and reproducibility than the conventional titrimetric method. Additionally, it was more straightforward and more economical than HPLC and LC-MS. Furthermore, the current qNMR method was applied to investigate different food supplements and additives regarding cystine quantity. As a result, four of eight food supplement samples were found to be inaccurately labeled or even with fake labeling, with the relative actual amount of cystine ranging from 0.3% to 107.2%. In comparison, all three food additive samples exhibited satisfactory quality (the relative actual amount of cystine: 97.0–99.9%). Notably, there was no obvious correlation between the quantifiable properties (price and labeled cystine amount) of the tested food supplement samples and their relative actual amount of cystine. The newly developed qNMR-based approach and the subsequent findings might help standardization and regulation of the cystine supplement market.