In structures with special geometry lattices, variations in stacking sequences are ubiquitous, yielding many novel structures and functionalities. Despite a wealth of intriguing properties and wide-ranging applications, there remains a considerable gap in understanding the correlation between special geometry lattices and functionalities in borides. Here, we design and synthesize a new superconducting boride Nb2IrB2, with a body-centered orthorhombic structure, consisting of alternating two-dimensional [Nb-Ir-Nb] triple-triangular-lattice-layers and B fragment layers. Advanced aberration-corrected scanning transmission electron microscopy observations show variable stacking configurations between [Nb-Ir-Nb] triple-triangular-lattice layers that can be tuned through synthesis conditions. Density functional theory calculations reveal that the coherent low-energy boundary interface plane of {101} between [11̅1] and [010] domains is responsible for the variable stacking behaviors. Energetically favorable structures are thereby reasonably proposed, based on nanoscale imperfect structure units. These findings provide valuable insights for designing and exploring new structures and functionalities within boride systems involving special geometry lattices.