The creation of p-n junction structure in photocatalysts is a smart approach to improve the photocatalytic activity, as p-n junctions can potentially act to suppress the recombination reaction. Understanding the surface conditions of the junction parts is one of the biggest challenges in the development of photocatalyst surface chemistry. Here, we show a relationship between the photocatalytic activity and potential gradient of the junction surface prepared from two-dimensional crystals of p-type NiO and n-type calcium niobate (CNO). The ultrathin (ca. 2 nm) junction structure and the surface potential were analyzed using low energy ion scattering spectroscopy and Kelvin probe force microscopy. The photocatalytic H-2 production rate for the n-p (CNO/NiO) junction surface was higher than those for p-n (NiO/CNO) junction, p, and n surfaces. The surface potential of the CNO/NiO junction part (surface: CNO) was lower than that of the CNO crystals in the same CNO crystal surface. These potential gradients result in specially separated reaction sites, which suppress the recombination reaction in the CNO nanosheet. Photo-oxidation and photoreduction sites in the junction structure were confirmed using the photodeposition reaction of MnOx and Ag.