The interface engineering of two-dimensional transition metal dichalcogenides (2D-TMDs) and metals has been regarded as a promising strategy to modulate their outstanding electrical and optoelectronic properties. Chemical Vapour Deposition (CVD) is an effective strategy to regulate the contact interface between TMDs and metals via directly growing 2D TMDs on a 3D metal substrate. Nevertheless, the underlying mechanisms of interfacial phase formation and evolution during TMD growth on a metallic substrate are less known. In this work, we found a 2D non-van der Waals (vdW) Mo-rich phase (MoNSN+1) during thermal sulfidation of a Mo-Au surface alloy to molybdenum disulfide (MoS2) in a S-poor environment. Systematic atomic-scale observations reveal that the periodic Mo and S atomic layers are arranged separating from each other in the non-vdW Mo-rich phase, and the Mo-rich phase preferentially nucleates between outmost 2D MoS2 and a 3D nanostructured Au substrate which possesses copious surface steps and kinks. Theoretical calculations demonstrate that the appearance of the Mo-rich phase with a unique metallic nature causes an n-type contact interface with an ultralow transition energy barrier height. This study may help understand the formation mechanism of the interfacial second phase during the epitaxial growth of 2D-TMDs on 3D nanostructured metals, and provide a new approach to tune the Schottky barrier height by the design of the interfacial phase structure at the heterojunction.