Clock transitions play an important role in extending the coherence time of rare-earth (RE) ion-doped crystals. It is still a challenge to accurately obtain the hyperfine structure of these crystals to determine their clock transitions and establish a proper solid-state quantum memory system. In this work, a nonspin-Hamiltonian method combining density functional theory (DFT)-based geometric optimization and effective Hamiltonian is utilized to obtain the hyperfine sublevels and clock transitions under an external magnetic field for the Kramers RE ion in crystals. To show clearly, the 173Yb3+:Y2SiO5 crystal is first investigated to demonstrate that the complicated hyperfine structure of the Kramers RE ion can be correctly calculated by the complete diagonalization (of energy) matrix (CDM) formalism. Second, optical and angular-dependent electron paramagnetic resonance (EPR) spectra of the 171Yb3+:Lu2Si2O7 crystal are studied by fitting calculations based on the DFT-optimized geometric structure. By reliable fitting parameters, the external magnetic field at clock transitions is determined successfully. Such two case studies indicate that the hyperfine structure and clock transitions of the Kramers RE ion in the crystal can be accurately predicted by the present approach. This is very useful for designing and searching practical RE-based quantum memory materials with longer optical or spin coherence time.