The measurement of environmental neutrons is particularly important in the search for new physics, such as dark matter particles, because neutrons constitute an often-irreducible background source. The measurement of the neutron energy spectra in the sub-MeV scale is technically difficult because it requires a very good energy resolution and a very high γ-ray rejection power. In this study, we used a super-fine-grained nuclear emulsion, called Nano Imaging Tracker (NIT), as a neutron detector. The main target of neutrons is the hydrogen (proton) content of emulsion films. Through a topological analysis, proton recoils induced by neutron scattering can be detected as tracks with sub-micrometric accuracy. This method shows an extremely high γ-ray rejection power, at the level of 3 × 10 7 γ cm −2 , which is equivalent to 3 years accumulation of environmental γ-rays, and a very good energy and direction resolution even in the sub-MeV energy region. In order to carry out this measurement with sufficient statistics, we upgraded the automated scanning system to achieve a speed of 250 g/year/machine. We calibrated the detector performance of this system with 880 keV monochromatic neutrons: a very good agreement with the expectation was found for all the relevant kinematic variables. The application of the developed method to a sample exposed at the INFN Gran Sasso surface laboratory provided the first measurement of sub-MeV environmental neutrons with a flux of (5.9 ± 1.2) × 10 −3 cm −2 s −1 in the proton energy range between 0.25 and 1 MeV (corresponds to neutron energy range between 0.25 and 10 MeV), consistent with the prediction. The neutron energy and direction distributions also show a good agreement.