The work aims to coat the kraft paper surface with modified environment-friendly coating agent to improve the flexible printing effect of water-based ink. With 15 μm rods, nanocellulose (CNC) and chitosan composite (CTS) anion starch coating agent was evenly coated on the kraft surface at 42 mm/s. The printing suitability of water-based ink printing on kraft paper before and after coating was compared. The results showed that the smoothness of the coated kraft paper increased by 28.6%. The gloss was nearly doubled. The resistance to tear was improved by 19.3%. The folding strength was improved by 15.2%. The water absorption was reduced from 196.2 g/m2 to 174.2 g/m2. The density of the printing pattern was apparently improved. The friction resistance was better. The antibacterial resistance of the kraft paper was also improved. CNC-CTS anion starch coating agent can effectively improve the mechanical properties of kraft paper, such as resistance to tear and folding strength, and optical properties, such as smoothness, gloss, and water resistance and antibacterial resistance, without increasing the pressure to the environment, thus improve the printing density and friction resistance of printing patterns and antibacterial resistance of printing product.