We report two new eclogite localities (at Kanayamadani and Shinadani) in the high‐P (HP) metamorphic rocks of the Omi area in the western most region of Niigata Prefecture, Japan, which form part of the Hida Gaien Belt, and determine metamorphic conditions and pressure–temperature (P–T) paths. The metamorphic evolution of the eclogites is characterized by a tight hairpin‐shaped P–T path from prograde epidote–blueschist facies to peak eclogite facies and then retrograde blueschist facies. The prograde metamorphic stage is characterized by various amphibole (winchite, barroisite, glaucophane) inclusions in garnet, whereas the peak eclogite facies assemblage is characterized by omphacite, garnet, phengite and rutile. Peak P–T conditions of the eclogites were estimated to be ~600°C and up to 2.0 GPa by conventional cation‐exchange thermobarometry, Ti‐in‐zircon thermometry and quartz inclusion Raman barometry respectively. However, the Raman spectra of carbonaceous material thermometry of metapelites associated with the eclogites gave lower peak temperatures, possibly due to metamorphism at different conditions before being brought together during exhumation. The blueschist facies overprint following the peak of metamorphism is recognized by the abundance of glaucophane in the matrix. Zircon grains in blueschist facies metasedimentary samples from two localities adjacent to the eclogites have distinct oscillatory‐zoned cores and overgrowth rims. Laser ablation inductively coupled plasma mass spectrometry U–Pb ages of the detrital cores yield a wide range between 3,200 and 400 Ma, with a peak at 600–400 Ma. In the early Palaeozoic, proto‐Japan was located along the continental margin of the South China craton, providing the source of the older population of detrital zircon grains (3,200–600 Ma) deposited in the trench‐fill sediments. In addition, subduction‐related magmatism c. 500–400 Ma is recorded in the crust below proto‐Japan, which might have been the source for the younger detrital zircon grains. The peak metamorphic age was constrained by SHRIMP dating of the overgrowth rims, yielding Tournaisian ages of 347 ± 4 Ma, suggesting subduction in the early Carboniferous. Our results provide clear constraints on the initiation of subduction, accretion and the development of an arc‐trench system along the active continental margin of the South China craton and help to unravel the Palaeozoic tectonic history of proto‐Japan.