We evaluate the prompt atmospheric neutrino flux including nuclear correction and B hadron contribution in the different frameworks: NLO perturbative QCD and dipole models. The nuclear effect is larger in the prompt neutrino flux than in the total charm production cross section, and it reduces the fluxes by 10%−30% depending on the model. We also investigate the uncertainty using the QCD scales allowed by the charm cross section data from RHIC and LHC experiments.