The atomic and electronic structures of inversion domain boundaries in Mn-Al dual-doped ZnO (Zn0.89Mn0.1Al0.01O) have been investigated. Using atomic-resolution scanning transmission electron microscopy, a head-to-head c-axis configuration and cation stacking sequence of || along the c-axis were observed at the basal-plane inversion domain boundary. Energy-dispersive X-ray spectroscopy and electron energy-loss spectroscopy revealed significant localization of Mn and minor localization of Al at the basal-plane inversion domain boundary. Based on experimental findings, a Mn-doped basal-plane inversion domain boundary slab model was constructed and refined by first principles calculations. The model is in agreement with atomic-resolution images. The local electronic density of states of the slab model basal-plane inversion domain boundary shows a hybridization of the Mn d and O p states within the valence band and localized Mn d states in the conduction band. The thermoelectric properties of Zn0.99-xMnxAl0.01O ceramics have been reported in a previous work. In this work, the effects of inversion domain boundaries on the thermoelectric properties are discussed. In comparison to Zn0.99-xMnxAl0.01O ceramics with x0.05, inversion domain boundaries in Zn0.89Mn0.1Al0.01O caused thermal and electrical conductivity reduction due to interface scattering of phonons and electrons. The Seebeck coefficient increased, suggesting electron filtering at inversion domain boundaries.