Lattice distortion and mass fluctuation are two long-believed potential mechanisms for the reduced lattice thermal conductivity in high-entropy ceramics (HECs). However, related studies remain unclear. Taking high-entropy diborides (HEBs) as the prototype, the lattice-distortion-driven reduced lattice thermal conductivity in HECs is uncovered, whereas the influence of mass fluctuation is neglectable. Specifically, two groups of HEBs are designed by regulating the long-believed mechanisms of lattice distortion and mass fluctuation based on machine-learning-potential-based molecular dynamics simulations. The theoretical and experimental results show that lattice distortion plays a pivotal role in modulating the lattice thermal conductivity of HEBs, while the influence of mass fluctuation is neglectable. Further studies find that the aggravation of lattice distortion enables the reduction of the lattice thermal conductivity through the decreased phonon velocity and Debye temperature resulting from the simultaneously enhanced scattering of strain field fluctuation and bond strength fluctuation. In addition, lattice distortion is found to lower the electronic thermal conductivity by competing with vacancies. The research unravels the long-standing mystery of the reduced lattice thermal conductivity in HECs and offers insightful guidance for developing HECs with ultra-low thermal conductivities.