Recently, nitrogen-doped carbon nanotubes (N-doped CNTs) have received great attention in nanocomposite design. It has become highly necessary to develop predictive models to elucidate their toughning behavior. In this study, the effects of CNTs with three different types of N-doped functional groups (quaternary, pyrrolic, and pyridinic) on the fracture toughness (FT) and crack growth of polymer nanocomposites are predicted using a multiscale analysis approach. To scale up from the nanoscale to the macroscale, a multiscale analysis approach integrating molecular dynamics, micromechanics theory, linear fracture mechanics theory, and a phase-field fracture model (PFFM) is adopted. The toughness enhancement trends of the three different types of N-doped functional groups were quantified by considering four toughening mechanisms (CNT debonding, plastic nanovoid growth, CNT pull-out, and CNT rupture), and compared with experimental result. The results show that the excellent interphase and interfacial properties of quaternary and pyridinic functional groups significantly improve the FT and crack growth resistance of N-doped CNT/epoxy nanocomposites. Our study provides high-performance solutions for experimental studies pertaining to the FT and crack growth of N-doped CNT/epoxy nanocomposites.