The Early Palaeozoic Shuanggou ophiolite is the best-preserved part of the Ailaoshan ophiolite belt. The microgabbros (basaltic dykes) and basalts (basaltic lavas) show distinct characteristics in geochemistry, implying that their genetic mechanisms are different. With Al2O3 contents ranging from 14.7% to 17.0%, the microgabbros belong to low-alumina type. They exhibit normal mid-ocean-ridge basalt (N-MORB) -like trace elemental characteristics with positive εNd(t) values (9.7–11.6) and slightly variable (87Sr/86Sr)i ratios (0.7036–0.7046). In contrast, the basalts have high Al2O3 contents (19.5–23.2%), therefore belonging to high-alumina type. A plagioclase-accumulation model is used to account for the high alumina contents. Moreover, the basalts have enriched MORB (E-MORB) -like trace element characteristics with lower εNd(t) values (6.4–8.0) and (87Sr/86Sr)i ratios (0.7032–0.7036). Their incompatible element ratios exhibit linear correlation with the isotopic data, which is probably related to the contribution of a mixed lithosphere–asthenosphere source. In summary, a two-stage model is proposed to explain the formation of the Shuanggou ophiolite: (1) at the continent–ocean transition stage, the basalts were generated by low-degree partial melting of the mixed mantle near a slow-spreading embryonic centre; and (2) at the mature stage of the Ailaoshan Ocean, the microgabbros were produced by moderate-degree partial melting of the depleted asthenospheric mantle.