Metal dissolution from the positive electrode and redeposition on the negative electrode is one of the well-known failure processes in lithium-ion batteries (LIBs). And it is necessary to take effective measures to prevent this kind of issue from happening. This study examines the Mn tolerance of electrolytes based upon lithium bis(oxalato)borate (LiBOB) and LiPF6. Results show that compared with LiPF6-based cell, the one based on LiBOB is impacted less by dissolved Mn2+ ions. When Mn concentration in electrolyte is less than 50ppm, the adverse effect of additive Mn2+ ions is tolerable, due to the excellent film-forming properties of LiBOB itself. However, when Mn concentration in LiBOB-based electrolyte is higher than 50ppm, a small amount of Mn ions are detected on the graphite electrode. Subsequently, continuous decomposition products of the electrolyte induced by the deposited Mn compounds may hinder the intercalation of lithium into the graphite, thereby reducing the reversibility of the lithium intercalation. This study suggests that LiBOB-based electrolyte is an alternative electrolyte for relatively low-cost manganese-based electrodes by improving Mn tolerance to some extent.