Seamount accretion is one of the most significant accretionary orogenic processes in the Central Asian Orogenic Belt, but there are few paleo-seamounts reported from and debate on the tectonic evolution of the Junggar Ocean still exists. In this study, we present geochronological, mineralogical, geochemical and isotopic data for basalts from the Chagantaolegai ophiolitic mélanges in Junggar. Zircon U-Pb dating on one basalt yielded a weighted mean 206Pb/238U age of 469 ± 7 Ma, which suggests that it formed in the Middle Ordovician. All rock samples belong to alkaline basalt and show similar geochemical characteristics, displaying high TiO2 (~3 wt%), (La/Yb)N (17.6–19.0), ΣREE (232–289 ppm) and enrichment in Nb and Ta, which implies an ocean island basalt (OIB) affinity. Based upon positive εNd(t) (+4.16 to +4.23), ΔNb (0.20–0.22) and low initial 87Sr/86Sr (0.70425 to 0.70452) and Zr/Nb (3.35–3.57), we suggest that the Chagantaolegai OIB samples were likely derived from a fertile mantle source related to plume. The OIB rock assemblage, chert and marble in the southern part of the Chagantaolegai ophiolitic mélange indicates that a Middle Ordovician seamount was accreted to the Boshchekul-Chingiz arc due to the northward subduction of the Junggar-Balkhash Ocean.