Eclogites from the Baijingsi area in the North Qilian orogen at NW China were analyzed for major and trace element abundances as well as Sr, Nd, and Hf isotope ratios to evaluate the impacts from subduction processes on these compositional parameters and to reveal the complexity in protolith characteristics. The major element compositions of the Baijingsi eclogites are within the ranges for basalts. However, the absence of systematic variations among major oxides indicates varying extents of metamorphic modifications. Seven samples are characterized by profound Nb and Ta depletions. Six of them form coherent trends in the La versus Th, HFSE, and LREE plots. They are classified as the Group 1 samples. Other eight samples, referred to as the Group 2 samples, define distinct La–Zr and La–Sm trends and have flat variation patterns with slight Th–Nb–Ta–LREE depletions in the primitive mantle-normalized multiple-element diagram. Group 1 dominates the 87Sr/86Sr–87Rb/86Sr, 143Nd/144Nd–147Sm/144Nd and 176Hf/177Hf–176Lu/177Hf trends for relatively larger variations in the isotope and abundance ratios. Based on the errorchron ages from the samples, closure temperatures of the isotope systems, and isotope ratio versus 1/X plots (e.g., 87Sr/86Sr–1/Sr), it is inferred that the Rb–Sr isotope system was subjected to metamorphic modification, whereas the Sm–Nd and Lu–Hf isotope systems mainly reflect protolith characteristics. In addition to the Nb and Ta depletions, the Group 1 samples generally have εHf(510) values (protolith initial at 510Ma) higher than those of MORB at a given εNd(510), reflecting derivation from relatively high Lu/Hf ratio sources. They also plot within the fields for arc lavas in the Ta/Yb–Th/Yb and Th–Ta–Hf/3 diagrams. All these features are consistent with derivation from protoliths of an arc origin. In contrast, the Group 2 samples have εNd(510) values slightly higher than those of the Group 1 samples at a given εHf(510), plotting on the low εNd(510) margin of the MORB field. They also deviate from the Ta/Yb–Th/Yb trend defined by MORB and OIB toward higher Th/Yb values within the fields of back-arc basin basalts. Therefore, it is inferred that the protoliths of the Group 2 samples were generated as back-arc basin basalts possibly associated with the protoliths of the Group 1 samples in a common supra-subduction zone. The εNd(510)–εHf(510) relationship of the Baijingsi eclogites shows an affinity to the Indian ocean type mantle, implying protolith generation at the southern hemisphere on the margin or a fragment of the Gondwana continent, most likely in the Qilian Block. Based on the current tectonic configuration, a southward subduction is required for protolith generation and might eclogitize the arc protoliths by subduction erosion. Alternatively, the northward subduction in a bidirectional subduction system might become dominant during the amalgamation of the Qilian Block and the North China Craton to eclogitize the arc protoliths in the Qilian Block. Resolving these two possibilities requires more petrological, geochemical, and structural evidence from the North Qilian orogen.