•The eclogites in the NQUB were metamorphosed from Neoproterozoic mafic rocks.•The protoliths of the Group 1, Group 2 and Group 3 eclogites have been generated by variable extents of mixing between enriched and depleted mantle components.•Neoproterozoic mafic magmatism in the Altun-Qilian-Kunlun orogenic belt could be the product of mantle plume activities. The North Qaidam ultrahigh-pressure metamorphic belt (NQUB) is distinguished by the widespread distribution of eclogites. However, the protolith nature of these eclogites remains controversial. This study reports new zircon LA-ICP-MS U–Pb ages and whole-rock geochemistry as well as Sr–Nd isotopic data on the Yuka and Dulan eclogites in the NQUB. Zircon U–Pb dating results of these eclogites indicate that the protolith and metamorphic ages are 831–809 Ma and 439–433 Ma. Based on distinct geochemical features, the samples can be classified into high-Ti/Y type (Group 1) and low-Ti/Y type (Group 2 and Group 3). The Group 1 eclogite protoliths are geochemically similar to oceanic island basalts (OIB) and likely originated from garnet-spinel peridotite mantle sources. The protoliths of Group 2 eclogites have a similar mantle source to those of the Group 1 protoliths, but experienced a higher degree of fractional crystallization and crustal contamination. The Group 3 eclogites have N-MORB-like affinity, and may be derived from shallower mantle sources in the spinel stability field. The differences in mantle sources of enriched (Group 1 and Group 2) and depleted (Group 3) eclogite protoliths can be ascribed to varying extents of mixing between enriched plume and depleted MORB-type mantle components at various melting depths. Our results suggest that the Neoproterozoic protoliths of eclogites in the NQUB belonged to a part of widespread Neoproterozoic rift-related mafic magmatism in the Altun-Qilian-Kunlun Orogenic Belt. These rocks could be the products of mantle plume activities that caused the breakup of Rodinia. Most Neoproterozoic mafic rocks in the NQUB experienced early Paleozoic HP/UHP metamorphism.