Bacterial cellulose nanocrystals (BCNC) have gained significant study attention in the field of anti-counterfeiting due to the advantages in viscosity regulation, suspension stability, printability, and shear-thinning behavior. In this study, a novel nanohybrids was developed by electrostatically self-assembling BCNC with lanthanide (Er, Yb)-nitrogen (N) co-modified graphene quantum dots (GQDs). These nanohybrids were then incorporated into a polyvinyl alcohol (PVA) waterborne ink, leveraging the unique rheological properties of BCNC to form a stable network architecture. The incorporation resulted in improved thixotropic behavior and increased yield stress of the PVA waterborne ink, thereby enabling a more systematic approach to the design and successful synthesis of a waterborne fluorescent ink used for dual anticounterfeiting purposes. The synthesized Er/Yb/N-GQDs demonstrated both photoluminescence (blue light) and upconversion luminescence (green light) characteristics upon excitation at wavelengths of 370 nm and 980 nm, respectively. Therefore, effective information extraction necessitated the concurrent use of two distinct excitation light sources, thereby heightened the difficulty of illicit counterfeiting. This study introduced a waterborne fluorescent dual anticounterfeiting ink with significant potential for applications in information security and identity authentication. Moreover, it served as a valuable reference for its adoption in the printing and packaging industries.