Bio-based flame retardants meet the requirements of environmentally friendly flame retardants. In this article, nitrogen and phosphorus-modified bio-based cellulose nanocrystals (CNCs) composite (NPCNCs) was designed and added into epoxy resin (EP) to measure flame retardancy and mechanical property. NPCNCs was successfully synthesized using ice bath polymerization and it exhibited a fibrous appearance with a rough surface, in which N and P elements were connected through hydrogen bonding. When corresponding into EP, NPCNCs endowed EP composite with excellent flame retardancy and smoke suppression. For the EP/6NPCNCs, the LOI value was 27.6% which was higher than that of pure EP (23.5%). Compared with pure EP, the THR, PHRR, TSP and PSPR value of composites decreased by 27.27%, 43.34%,70.21% and 66.67%. This was attributed to catalysis-dehydration and carbonization, carbon support of CNCs, gas phase dilution. In addition, the mechanical property of the EP composites was analyzed, and the results showed that the mechanical properties were basically maintained compared with the pure EP. This article will provide a new way for the design bio-based P and N-modified flame retardants.