Using first-principles calculations in the generalized gradient approximation plus on-site Coulomb interaction (GGA+U) scheme, the effects of internal structural parameters x and U on the electronic structure of YbB₆ are investigated. The results show that the band gap of YbB₆ increases with x increasing, and does not change with U. It not only illustrates the influence of internal structural parameter x on band gap, but also explains the discrepancy between the previous experimental result and the theoretical prediction. In addition, the electronic structure and density of states reveal that there exist the interactions between B atoms in different cages, and that a small band gap can form around the Fermi level (E _F). The present work plays a leading role in ascertaining the relation between crystal structure and electronic property for the further analysis of its topological properties.