Carbon nanotubes (CNTs) display unique properties and have many potential applications. Prior theoretical studies on CNTs are based on atomistic models such as empirical potential molecular dynamics (MD), tight-binding methods, or first-principles calculations. Here we develop an atomistic-based continuum theory for CNTs. The interatomic potential is directly incorporated into the continuum analysis through constitutive models. Such an approach involves no additional parameter fitting beyond those introduced in the interatomic potential. The atomistic-based continuum theory is then applied to study fracture nucleation in CNTs by modelling it as a bifurcation problem. The results agree well with the MD simulations.