High-dimensional entanglement not only offers a high security level for quantum communication but also promises improved information capacity and noise resistance of the system. However, due to various constraints on different high-dimensional degrees of freedom, whether these advantages can bring improvement to the actual implementation is still not well proven. Here we present a scheme to fully utilize these advantages over long-distance noisy fiber channels. We exploit polarization and time-bin hyperentanglement to achieve high-dimensional coding, and observe significant enhancements in secure key rates and noise tolerance that surpass the capabilities of qubit systems. Moreover, the demonstration achieves a distribution up to 50 km, which is the longest distance for high-dimensional entanglement-based quantum key distribution up to date, to our knowledge. Our demonstration validates the potential of high-dimensional entanglement for quantum communications over long-distance noisy channels, paving the way for a resilient and resource-efficient quantum network.