Among sub-nanometer clusters, boron-based clusters and their atom-doped counterparts have attracted great attention due to their mechanical, physical, and chemical properties as well as their applications. Molecular dynamics (MDs) simulations and ab initio methods, including density functional theory (DFT) calculations, have been used to understand the physical and chemical properties of different materials. Much research has recently been conducted by using various methods to determine the different properties of boron clusters. In this chapter, we briefly introduce the relevant modeling and simulation methods, then review very recent theoretical researches on the application of small boron clusters, such as gas sensors, electrodes, H2 storage, drug delivery, and catalytic applications.