Trivalent praseodymium (Pr3+)-doped yttrium silicate (Y2SiO5) crystals have been widely used in various phosphors owing to their excellent luminescence characteristics. Although a series of studies have been carried out on its application prospects, the electronic structures and energy-transfer mechanisms of Pr3+-doped Y2SiO5 (Y2SiO5:Pr) remain an exploratory topic. Herein, the crystal structure analysis by the particle swarm optimization structure search method is used to study the structural evolution of Y2SiO5:Pr. Two novel structures with local [PrO7]-11 and [PrO6]-9 [Y2SiO5:Pr (I) and Y2SiO5:Pr (II)] are successfully identified. The impurity Pr3+ ions occupy the Y3+ sites and successfully integrate into the Y2SiO5 host crystal with a Pr3+ concentration of 6.25%. The calculated electronic band structures show that the doping of Pr3+ induces a reduction in band gaps for the host Y2SiO5 crystal. The conduction bands near the Fermi level are completely composed of f states. For the atomic energies of Pr3+ in Y2SiO5, the Stark levels and transitions are properly simulated based on a new set of crystal field parameters (CFPs) at the C1 site symmetry. A satisfactory r.m.s. dev. of 15.57 cm-1 with 9 free ion parameters (plus 27 fixed CFPs as obtained from ab initio calculation) fitted to the 33 observed levels is obtained for the first time. The plentiful energy-level transition lines, from the visible light to the near-infrared region, are deciphered for Pr3+ in Y2SiO5. Blue 3P0 → 3H4 at 465 nm is calculated to be a strong emission line, and it might be an ideal channel for laser actions. These results could not only provide important insights into the rare-earth-doped crystals but also lay the foundation for future research studies of designing the new laser materials.