The work aims to prepare water-based carbon dot fluorescent ink with citric acid carbon dots (CDs) as the fluorescent, so as to provide reference for the further application of such ink in anti-counterfeiting packaging and fluorescent biosensor. Firstly, CDs were prepared by high temperature pyrolysis with citric acid as the carbon source. Then, the as-prepared CDs were used as the fluorescent pigment, ethanol solution as the connecting material, sodium carboxymethyl cellulose as the binder and stabilizer, and polyvinylpyrrolidone solution as the surfactant to prepare water-based carbon dot fluorescent ink. High power transmission electron microscopy (TEM) scanning showed that the structure of the prepared CDs was regular and spherical, the particle size was 1.2-1.8 nm, and there was no obvious aggregation in aqueous solution, demonstrating that the distribution of the CDs in water was uniform. Besides, the as-prepared CDs emitted blue light when excited by 365 nm UV, and the fluorescence emission spectrum presented obvious excitation wavelength dependence. Based on the above-mentioned CDs, the water-based fluorescent ink was brown-yellow under visible light and showed good wettability to ordinary printing paper. The as-prepared fluorescent ink has fluorescence property, with fluorescence emission wavelength not changing with the excitation wavelength and shows good wettability to ordinary printing paper. The research results have a certain reference value for the application of biogenic carbon dots-based fluorescent ink in biosensors and anti-counterfeiting.