Lithium‑sulfur (Li-S) batteries have been recognized as one of the promising energy systems which can meet the large amounts of energy demanding. However, its practical application has been seriously hindered due to the instinct drawbacks such as low conductivity, large volume expansion and notorious “shuttle effect”. Herein, multi-structure lamellar flower-like zinc vanadate/zinc oxide heterojunction (CoNi@ZnV2O4/ZnO-N,C) with abundant oxygen vacancies, CoNi nanoalloys and N-doped carbon (C) layer has been successfully constructed. XPS and ex-situ XRD analysis reveal that the oxygen vacancies can replace lattice oxygen to adsorb lithium polysulfides (LPS), then stabilize the crystal structure. Additionally, with the synergistic catalysis of CoNi nanoalloys and N-doped C layer, the heterojunction can effectively accelerate the conversion of LPS and promote the precipitation of Li2S. When the lamellar flower-like heterojunction is applied as separator modifier, the “shuttle effect” of LPS can be effectively hindered, leading to synergistic enhancement of long cycle performance of Li-S batteries: the initial discharging capacities of 1468.9 and 1394.9 mAh g−1 can be obtained at 0.1 and 1C, respectively. After 1000 long-term cycles at 3C, the discharging capacity can be still maintained at 467.9 mAh g−1, with a capacity loss rate of 0.049 % per cycle, showing a stable high-rate performance.