Increased interest in two-dimensional (2D) materials and heterostructures for use as components of electrical devices has led to the use of an atomically mixed phase between semiconducting and metallic transition metal dichalcogenides that exhibited enhanced interfacial characteristics. To understand the lattice structure and properties of 2D materials on the atomic scale, diverse characterization methods such as Raman spectroscopy, high-resolution transmission electron microscopy (HR-TEM), and X-ray photoemission spectroscopy (XPS) have been applied. However, determination of the exact chemical distribution, which is a critical factor for the interfacial layer, was hindered by limitations of these typical methods. In this work, atom-probe tomography (APT) was introduced for the first time to analyze the three-dimensional atomic distribution and composition variation of the atomic-scale multilayered alloy structure W NbSe. Composition profiles and theoretical calculations for each atom demonstrated the reaction kinetics and stoichiometric inhomogeneity of the W NbSe layer. The role of the intermediate layer was investigated by fabrication of a WSe-based field-effect transistor. Introduction of W NbSe between metallic NbSe and semiconducting WSe layers resulted in improved charge transport with lowering of the contact barrier.