As an intermediate transition state between atoms/molecules and bulk materials, cluster nanostructures are usually different from macroscopic substances and superior to standard elements. In the past two decades, a combination of cluster prediction algorithms and experimental spectroscopy techniques has thoroughly explored the ground state structures of pure boron clusters and metal-doped boron clusters. The fruitfulness of this dual approach well illustrated the intriguing microstructure and unique physicochemical properties of pure boron clusters and metal-doped boron clusters caused by the inherent electron-deficient properties of boron element, such as aromaticity and chemical bond fluxionality. We start with an overview of the several classical geometric configurations of pure boron clusters in a wide range, such as planar, nanotube, bilayer, fullerene-like and core-shell. Furthermore, we describe the recent advances in single or multiple metal atom doped boron clusters, focusing on the modification of the geometric and electronic structures of pure boron clusters by heteroatom. Finally, we discuss the possibility of constructing boron-based nanomaterials with specific functions from metal boron clusters. Despite the fruitful results of boron cluster studies, boron-based chemistry has not yet reached its peak. Further exciting discoveries of new intriguing structures and electronic properties continue to evolve, which is the foundation for new boron-containing compounds.