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Subduction zones are critical sites for recycling of Li and B into the mantle. The way of redistribution of Li and B and their isotopes in subduction settings is debated, and there is a lack of detailed studies on Li and B partitioning between minerals of different types of eclogites and the host rocks of the eclogites. We present Li and B concentration data of minerals and Li and B whole-rock isotope data for low-T and high-T eclogites and their phengite schist host rocks from the Changning–Menglian suture zone, SW China. Omphacite controls the Li budget in both the low-T and high-T eclogites. Low-T eclogites have Li and δ7Li values (8.4–27.0 ppm, – 5.5 to + 3.2 ‰) similar to the phengite schists (8.7–27.0 ppm, – 3.8 to + 3.0 ‰), suggesting that Li was added to low-T eclogites from the phengite schists. In contrast, high-T eclogites have much lower δ7Li values (– 13.2 to – 5.8 ‰) than the phengite schists, reflecting prograde loss of Li or exchange with wall rocks characterized by low δ7Li values. Phengite and retrograde amphibole/muscovite are the major B hosts for low-T and high-T eclogites, respectively. The budgets and isotopic compositions of B in eclogites are affected by the infiltration of fluids derived from phengite schists, as indicated by eclogite δ11B values (– 15.1 to – 8.1 ‰) overlapping with the values of the phengite schists (– 22.8 to – 9.5 ‰). Lithium and B in eclogites are hosted in different mineral phases that may have formed at different stages of metamorphism, implying that the contents and isotopic compositions of Li and B may become decoupled during subduction-related fluid-mediated redistribution. We suggest a mineralogical control on the redistribution of Li and B in eclogites during subduction and the exchange of Li and B with the immediate wall rocks. The observed contrasting Li and B isotopic signatures in eclogites are likely caused by a fluid-mediated exchange with different types of wall rocks during both prograde metamorphism and exhumation.