Carbon dots (CDs) rank among the most promising luminescent nanomaterials for anti-counterfeiting application owing to their high fluorescence quantum yield and nontoxicity. Herein, we report a novel, high-level security performance anti-counterfeiting strategy achieved by fluorescence-lifetime-encoded CD fluorescent inks. CD-inks have identical steady-state emission properties, but they have distinctive and well-separated fluorescence lifetimes, allowing authentication of security tags using exclusively fluorescence lifetime imaging. A proof-of-concept anti-counterfeiting tag using CD-based lifetime-encoded inks is demonstrated. The developed CD lifetime-based anti-counterfeit technology is awaited to be applicable to a wide spectrum of security-protecting purposes. Furthermore, the presented method can be easily extended to integrate fluorescence-lifetime-encoded CDs in multichannel bioimaging, high-throughput flow cytometry, and optical data storage.