In an effort to make rational use of resources, wasted bagasse were collected, and then fabricated by layer-by-layer (LbL) assembly to prepare an environmentally benign flame retardant for epoxy resin (EP). Six chitosan/ammonum polyphosphate bilayers were successfully deposited on the surface of bagasse, which endows EP/6BL@BF composites with a limiting oxygen index value of 24.1% and V-1 rating in UL-94 test. Compared with untreated bagasse, cone calorimetry test reveals that the incorporation of 6BL@BF reduces the peak heat release rate and total heat release by 64.6% and 13.2%, respectively. Besides, expandable graphite (EG) was combined with 6BL@BF to further enhance the fire safety and thermal stability of EP composites. Furthermore, the gas and condensed phase analysis of EP/6BL@BF/EG-3 composite was investigated by TG-IR, scanning electronic microscopy, Laser Raman spectroscopy, and X-ray photoelectron spectroscopy, and the flame retardant mechanism of 6BL@BF/EG was proposed. Finally, the mechanical properties of EP composites were investigated systematically.