The electronic contribution significantly dominates thermal transport for most pure metallic systems, while the phononic (lattice) contribution remains relatively small. We report four metallic materials, namely cubic BeCo, BeNi, BeRh, and BeHf, which are screened by our recent deep learning approach from Open Quantum Materials Database, all possessing large phonon bandgaps and phonon anomaly features. Employing first-principles calculations to solve the phonon Boltzmann transport equation, we report that at room temperature, the phononic thermal conductivity of these Be-X compounds is exceptionally high, rivaling that of diamond. Specifically, the thermal conductivities are 2117 W/mK for BeCo, 2243 W/mK for BeNi, 2368 W/mK for BeRh, and 1600 W/mK for BeHf. This remarkable thermal performance is attributed to the large phonon bandgaps and phonon anomaly features present in these materials. Furthermore, when electron-phonon coupling is accounted for, the phononic thermal conductivities of the Be-X compounds experience a reduction by approximately 2 orders of magnitude. Notably, BeHf presents an exceptional case, with its phononic thermal conductivity measured at 68 W/mK. This value is several times to an order of magnitude higher than the typical range observed in most metals and metallic systems, which generally lies between 2 and 18 W/mK. Quantitative analysis of phonon lifetime, Eliashberg spectral function, and Fermi surface show that the Be-X systems have strong electron-phonon coupling which originates from their Fermi surface nesting. However, the phonon anomalies of BeHf are shallower, which weakens the electron-phonon coupling and results in the abnormally high phononic thermal conductivity of BeHf. This research enhances our comprehension of various heat conduction phenomena in crystals, particularly offering a method to identify new materials with phonon-mediated thermal transport in metals and metallic systems for innovative applications in the future.