Battery energy storage stations (BESSs) hold promising market potential within microgrids, serving as a complementary solution to mitigate fluctuations in renewable distributed generations and providing backup power during microgrid outages or emergencies. However, the distinct fault signatures of BESSs, compared to conventional synchronous generator (SG)-based sources, can result in misoperation of the widely-used superimposed current magnitude (SCM)-based faulty phase selector (FPS), which has received limited attention in previous research. Moreover, the variable operation modes of the microgrid further deteriorate the working condition of the SCM-based FPS. As a consequence, the potential misidentification of faulty phase(s) in the presence of BESS violates the selective phase tripping requirements in existing microgrids. To achieve precise selection of faulty phase(s), this paper proposes a novel FPS based on the generalized magnitude ratio (GMR). Firstly, the proposed FPS applies a compensation method to SCM and extends it to the superimposed voltage magnitude (SVM), mitigating the adverse impacts caused by the unbalanced sequence impedance of BESS. Subsequently, the GMR, which integrates both the compensated SCM and SVM information, is constructed to enhance the adaptability of phase selection to the uncertain infeed level at the BESS side. Finally, the faulty type and specific faulty phase(s) are determined based on the sorted results of the GMR values for each phase. Comprehensive simulation results affirm the expected performance of the proposed FPS under various microgrid modes, as well as different BESS discharge/charge statuses.