Boron nanoclusters and few‐layer borophenes have received considerable attention in recent years due to their unique structural and bonding patterns. Based on extensive global searches and density‐functional theory calculations, we present herein the possibility of a new series of bilayer medium‐sized boron clusters including C2 B54 (I), C2h B60 (II), and C1 B62 (III) in a universal structural pattern, with one, two, and three B6 hexagonal windows on the waist around a B38 bilayer hexagonal prism at the center, respectively. Detailed orbital and bonding analyses indicate that these three‐dimensional aromatic bilayer clusters follow the σ + π double delocalization bonding pattern, with three or four effective interlayer B–B σ‐bonds formed to further stabilize the system. The IR, Raman, and UV/Vis spectra of the bilayer species are theoretically simulated to facilitate their future spectral characterizations.