Recent research is keen to introduce biomass materials into inks to develop "green" printing, but little attention has been given to whether these inks can be truly widely used in printing industry. There are few bio-based inks suitable for low surface energy plastic such as polyethylene glycol terephthalate (PET), which is one of the most common printing substrates. Herein, waterborne polyurethane with polyfluoroalkyl side chain (F-WPU) was designed and synthesized to prepare fluorocarbon quantum dots (F-CDs). F-WPU and F-CDs were mixed together with gelatin to obtain environmentally friendly inks which were utilized to print on a low surface energy substrate. F-WPU (30 wt%) and F-CDs (0.5 wt%) significantly improve the mechanical properties of composites by forming an interpenetrating network system and hydrogen bonds, respectively. Abundant carbon-fluorine bonds effectively reduce the surface energy of gelatin, resulting in excellent hydrophobicity and strong adhesion to the PET surface. The thermal stability of the composite could significantly enhance to meet the promising needs for the further engineering applications. Besides, F-CDs could emit blue-green fluorescence based on conjugated structure and π→π* transition under a wider excitation wavelength. Therefore, the complex exhibited good transparency under sunlight and performed significant cyan fluorescence under an ultraviolet irradiation, in which can be efficiently developed and used in anti-counterfeiting labels and printing. Furthermore, the friction, soaking and kneading tests have been measured to seriously take the considerations for the stable dry and wet fastness for the PET films, which could industriously expand the ink applications.