Microphase-separated structures of a poly(deuterated styrene-block-2- vinylpyridine) (dPS-b-P2VP) block copolymer in thin films were studied by neutron reflectivity (NR) and transmission electron microtomography (TEMT). The dPS-6-P2VP block copolymer shows a cylindrical morphology in the bulk state. The block copolymer was spun-coated on a Si substrate, which was extensively annealed (170°C for 14 days) before the NR experiments. The annealed thin film showed a featureless NR profile, the reflectivity monotonically decreased with the increasing scattering vector along the depth direction of the thin film, qz. The portion of the dPS-b-P2VP block copolymer thin film used in the NR experiment was examined by TEMT, from which a three-dimensional (3D) morphology of the block copolymer thin film was successfully obtained. The 3D image clearly showed that the microphase-separated structure inside the thin film had a cylindrical morphology with some order along the depth but almost no in-plane order. In order to analyze the NR profile by a conventional model fitting method, a model structure that exhibits a concentration profile is necessary as an initial "guess". In this study, two different models i. e., (i) hexagonally packed P2VP cylinders laying parallel to the Si substrate based on the known lattice parameters and (ii) experimentally obtained TEMT 3D structure, were proposed. The concentration profiles evaluated from these two models were used as the initial guesses in the fitting of the calculated profiles to the experimentally obtained NR profile, Rexp. It was found that the fitting based on the former model failed, while the fitting based on the latter one had an excellent fit to the Rexp. This result demonstrates that the microphase-separated structures that are NOT perfectly periodic nor oriented can still be analyzed by our new technique.