The discovery of borospherene B₄₀ leads to a new beginning for the study of boron chemistry and may lead to new boron-based nanomaterials. Based on density functional theory, the structures, electronic properties, infrared and Raman spectra, photoelectron spectra, and electronic absorption spectra of endohedral borospherenes M@B₄₀^0/– (M = H₂, HF, and H₂O) are investigated. It is found that H₂, HF, and H₂O monomers can form stable endohedral borospherenes M@B₄₀^0/– (M = H₂, HF, and H₂O). In addition, the calculated results indicate that the doped molecule at the off-center location can relax to the center location within the cage and the symcenter of the doped molecule is almost located in the center of the cage. Unlike endohedral metalloborospherene Ca@B₄₀, which is a charge-transfer complex between Ca²⁺ and B₄₀^2–, natural population analyses and chemical bonding analyses reveal that there is no significant charge transfer of the doped molecule. The calculated spectra indicate that doping of a molecule (H₂, HF, or H₂O) in borospherene B₄₀ can change the photoelectron spectra and doping of a polar molecule (HF or H₂O) in borospherene B₄₀ can change the spectral properties. For instance, the addition of a molecule can increase infrared and Raman-active modes and cause a red shift or blue shift of electronic spectra. These spectral features can be compared with future experimental values of endohedral borospherenes M@B₄₀^0/– (M = H₂, HF, and H₂O).