Various spectroscopic properties of Yb3+-doped YSiO5 crystal have been extensively investigated due to its promising application in quantum information processing. However, the local structure, electronic structure of Y2SiO5 crystal, and its optical and magnetic properties have not been comprehensively studied from a theoretical viewpoint. In this work, the geometric and electronic structures of Yb(3)that replaces two crystallographic Y3+ sites in the YSiO5 crystal are first obtained by the method of density functional theory (DFT). Then, the optical, electron paramagnetic resonance (EPR), and optically detected magnetic resonance (ODMR) spectra for(1)Yb(3+) (nuclear spin I = 1/2) at such two sites are simultaneously calculated in the framework of the complete diagonalization (of energy) matrix (CDM) based on the optimized local structure around Yb-171(3+) ion by DFT. The various calculated spectroscopic properties by such combined theoretical approach are consistent with the experimental ones, which demonstrates that CDM is effective and particularly suitable for calculating hyperfine A-tensors under zero, low, and intermediate magnetic field. More importantly, based on the obtained accurate hyperfine structure of Yb-171(3+) in YSiO5 crystal, the possible clock transitions, which can enhance the optical coherence time, can be assigned or predicted by the present approach. This study successfully explains the spectroscopic properties of Yb3+-doped YSiO5 and provides a feasible method to design and search for practical rare-earth-doped quantum information materials for the community.