West Junggar is located at the southwest margin of the Central Asian Orogenic Belt and includes Silurian pillow basalts of the Mayilashan Formation. The petrogenesis and tectonic setting of these pillow basalts are important for the understanding of the tectonic evolution and metallogeny of the West Junggar area. This paper presents geochronological, geochemical, and whole‐rock Sr–Nd–Pb isotope data from the pillow basalts of the Mayilashan Formation. Zircon LA‐ICP‐MS U–Pb dating of a pillow basalt, which is in conformable contact with the chert, suggests that they were erupted at 437.2 ± 2.2 Ma marking the timing of generation of these rocks as Middle Silurian. Geochemically, all the pillow basalts bear the signature of ocean island basalt (OIB), and are characterized by alkaline affinity with high concentrations of TiO2 (3.28–4.12 wt.%), LILE and LREE enrichment and HREE depletion ((La/Yb)N = 5.5–7.3), with very weak Eu anomalies (Eu/Eu* = 0.96–1.06), and no obvious Nb, Ta, or Ti negative anomalies. Their Sr–Nd–Pb isotopic compositions ((87Sr/86Sr)I = 0.7037–0.7051, εNd(t) = 1.9–2.9, 206Pb/204Pbi = 17.74–18.22, 207Pb/204Pbi = 15.48–15.52, and 208Pb/204Pbi = 36.49–37.86) show Dupal‐like isotopic signature of ophiolites in the southern Paleo‐Asian Ocean. These characteristics indicate that the magmas were derived from a deep OIB reservoir, that is, a depleted but slightly heterogeneous asthenospheric mantle source with ~5–15% partial melting of garnet and spinel lherzolite. Our obtained results, in conjunction with previous published data, allow us to suggest that the alkaline pillow basalts formed in a seamount within an intraoceanic setting, where a larger number of seamounts with different ages occurred in the Paleo‐Asian Ocean.