Zr doped boron carbide (B4.3C) semiconductor was prepared by hot pressing of mixture of boron carbide powder (B4.3C) and Zr nanocrystals (0.5 at %), to investigate influence of impurity incorporation on the subtle structure of B4C crystals. XRD analyses indicated that the hot-pressed sample was composed of B4.3C, (BN)4H, and (ZrB2)3H. Zr introduction does have modified the B4.3C structure. Especially, remarkable vacancies were led into on the B(3) sites of the C-B-C chain centre. The effect of Zr incorporation seems to be unique because similar structural change was not observed by the same experimental procedure with Ni doping. XPS studies revealed that the Zr atoms existed in a state with unsaturated bonding. B4.3C with interstitial Zr atoms is speculated.