The igneous units of Permian Tarim Large Igneous Province (TLIP) is typically characterized by alkaline affinity. Here we report for the first time the petrological, geochemical and isotopic characteristics of phonotephrite and phonolite dykes from the Wajilitag complex in the northwestern margin of the TLIP. Our data, especially Sr-Nd-Mg isotopes, suggest that the dykes have different mantle sources. Phonotephrite with mantle-like Mg isotope values (−0.295 to −0.382 ‰), relatively enriched Sr isotopes (0.70487 to 0.70574) and slightly lower ε_Nd(t) values (−0.23 to +2.06), were possibly derived from a lithospheric mantle source that was metasomatized by calcitic carbonate melt. The phonotephrites are highly evolved rocks formed through fractional crystallization from a parental magma which is similar to that of the mafic–ultramafic intrusions. Phonolites show relatively depleted Sr isotopes (0.70362 to 0.70409), higher ε_Nd(t) values (+1.27 to +3.45), markedly lighter Mg isotopes (−0.851 to −0.906‰) than the normal mantle indicating a mantle plume source with the involvement of carbonated eclogite. The parental magma of phonolites may be related to the liquid immiscibility with calciocarbonatites present in the Wajilitag complex due to their similar extremely light Mg isotopic compositions. The distinct geochemical features between two series of dykes in the Wajilitag complex reflect the diversity of mantle source of the TLIP, and their Sr-Nd-Mg isotopic characteristics indicate the role of subducted recycled sedimentary carbonates at different depths in the mantle.