Cotton fabrics with the main constituent of cellulose, which is hydrophilic, bacterial infected, and flammable, are in urgent need of functionalization as a kind of widely applied material. To address these issues, in this work, modified polyelectrolyte complex (MPEC) coatings with polyethylenimine (PEI), polyphosphate (APP), and perfluorodecyltrichlorosilane modified PEI (PFTS-PEI) are prepared to construct multi-functionally gradient MPEC coatings on cotton fabrics. Stability and synergistic effects on hydrophobicity, antibacterial activity, and flame retardancy in this system have been studied. Notably, PFTS-PEI with fluorine and silicone elements are confirmed to provide hydrophobicity and durability for MPEC coatings, which not only has no negative effect on other functions but also makes some improvement in antibacterial activity. This MPEC-treated cotton fabric finally has an antibacterial rate against S. aureus and E. coli of 99.9% and 96.9%, limiting oxygen index of 28.5% and water contact angle of 118°, which can be almost maintained after 20 times washing. The modified PEC will provide an efficient strategy to achieve durable multi-functions on cellulose-based fabrics.