AbstractRecent technological advances in the noisy intermediate‐scale quantum (NISQ) era are promising. Optically addressable color centers in semiconductors can achieve spin localization and are the most promising spin qubit candidates for NISQ technologies. Exploring a suitable and scalable atomic‐like color center is a prerequisite in this context. Here, a symmetry‐protected two‐level system (qubit) derived from a set of naturally separated Bell states in the H₃ center with C_2v symmetry is characterized. The characterized qubit significantly reduces magnetic noise compared with a degenerate triplet in C_3v systems for conventional qubits. The Hamiltonian, including the Coulomb interaction, spin–orbit coupling, and spin–spin interaction, is comprehensively developed using a combination of first‐principle calculations and group theory analyses. Consequently, an intrinsic spin–phonon interface embedded in an optical spin‐polarization loop can enable an effective interrogation of the information of the two‐level system. This study not only paves the way for developing further quantum information science applications utilizing the H₃ center but also provides a competitive qubit candidate for the NISQ era.