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The energy loss near edge fine structures of the B-K edge and O-K edge have been examined in the optical material YBa3B9O18. The orientation-dependent electron energy-loss spectra (EELS) for both B-K edge and O-K edge were observed. The experimental results were analyzed based on density functional theory calculations. The unoccupied pz features dominated the EELS when it was collected under the energy transfer q along c orientations and pxy states were probed when q was perpendicular to the crystallographic c axis. The results provide direct experimental evidence on the anisotropic characteristic of YBa3B9O18.