This work demonstrated a facile and sustainable approach to functionalize cellulose nanopaper (CNP) by impregnation of chitosan (CS) and the followed halogenation. It was found that the tensile strength of the functionalized CNP (CNP/CS-Cl) was enhanced by 38.3% and 512.6% at dry and wet conditions, respectively. Meanwhile, the total transmittance (at 550 nm) of CNP/CS-Cl was increased from 75% of pure CNP to 85%, with 35% decrease in optical haze. Moreover, the CNP/CS-Cl exhibited significant enhancement in barrier properties. Importantly, part of the amino groups on CS were transformed into N-halamines during the halogenation process, which endowed the CNP/CS-Cl with excellent antibacterial performance against both S. aureus and E. coli with 100% bacterial reduction after 10 min of contact. Thus, this work provides a simple and efficient approach to functionalize CNP with water resistance, high transparency, excellent antibacterial and barrier properties, which will expand the potential applications of CNP.