The relationship between the Shangdan and Erlangping suture zone (ESZ) and the initiation stretch time of the Early Paleozoic back‐arc system in the Qinling Orogen still remains unclear. This paper reports the chronological and geochemical data of the Miaogou mafic intrusion along the southern margin of the Shangdan suture. The pyroxenite in the mafic intrusion has a zircon U–Pb age of 485 ± 5 Ma (Mean Standard Weighted Deviation (MSWD) = 0.08, n = 18). It has low SiO2 (45.41–46.02 wt%), K2O (0.42–0.44 wt%), and TiO2 (0.73–0.83 wt%) contents, high MgO (13.9–15.13 wt%) contents with high Mg# (74–77). In combination with its high clinopyroxene portion, the pyroxenite represented the accumulates from the mafic magma. Some sieve rims of the clinopyroxene indicate that the primitive pyroxenite was metasomatized by subduction‐related fluids. However, their consistent trace element and rare earth element (REE) patterns suggest that the metasomatism process has insignificant effects on their geochemical features. Zircons from the pyroxenite have positive εHf(t) (+7.18 to +11.75) values, reveal a depleted source region. In combination with its high V (322–1,093 ppm) contents, low Ti/V (10–15) ratios and smooth REE patterns, we propose that the pyroxenite was derived from metasomatized depleted mantle wedge in a back‐arc basin. In considering the duration limit (<475 Ma) of the back‐arc basin along the ESZ, we argued that the ~485 Ma Miaogou pyroxenite represented the initiation back‐arc basin in the Shangdan suture, which might represent the initial rifting of the North Qinling microcontinent induced by the northward subduction of the Shangdan Ocean.