High-quality long-distance entanglement is essential for both quantum communication and scalable quantum networks. Entanglement purification is to distill high-quality entanglement from low-quality entanglement in a noisy environment and it plays a key role in quantum repeaters. The previous significant entanglement purification experiments require two pairs of low-quality entangled states and were demonstrated in tabletop. Here we propose and report a high-efficiency and long-distance entanglement purification using only one pair of hyperentangled state. We also demonstrate its practical application in entanglement-based quantum key distribution (QKD). One pair of polarization spatial-mode hyperentanglement was distributed over 11 km multicore fiber (noisy channel). After purification, the fidelity of polarization entanglement arises from 0.771 to 0.887 and the effective key rate in entanglement-based QKD increases from 0 to 0.332. The values of Clauser-Horne-Shimony-Holt inequality of polarization entanglement arises from 1.829 to 2.128. Moreover, by using one pair of hyperentanglement and deterministic controlled-NOT gates, the total purification efficiency can be estimated as 6.6×10^{3} times than the experiment using two pairs of entangled states with spontaneous parametric down-conversion sources. Our results offer the potential to be implemented as part of a full quantum repeater and large-scale quantum network.