Due to its unusual optical properties, neodymium ion (Nd3+)-doped bismuth silicate (Bi4Si3O12, BSO) is widely used for its excellent medium laser amplification in physics, chemistry, biomedicine, and other research fields. Although the spectral transitions and luminescent mechanisms of Nd3+-doped BSO have been investigated experimentally, theoretical research is severely limited due to the lack of detailed information about the microstructure and the doping site of Nd3+-doped BSO, as well as the electric and magnetic dipole transition mechanisms. Herein, we systematically study the microstructure and doping site of Nd3+-doped BSO using an unbiased CALYPSO structure search method in conjunction with first-principles calculations. The result indicates that the Nd3+ ion impurity occupies the host Bi3+ ion site with trigonal symmetry, forming a unique semiconducting phase. Based on our newly developed WEPMD method, the electric dipole and magnetic dipole transition lines, including a large number of absorption and emission lines, in the region of visible and near-infrared spectra of Nd3+-doped BSO are calculated. It is found that the (4)G(5/2) -> I-4(9/2), H-2(9/2) -> I-4(9/2), and F-4(3/2) -> I-4(11/2) channels are promising laser actions of Nd3+-doped BSO. These findings indicate that Nd3+-doped BSO crystals can serve as a promising multifunctional material for optical laser devices.