The development of new electrode materials for lithium-ion batteries (LIBs) is of great interest because available electrode materials may not meet the high-energy demands for electronic devices, especially the demands for good cyclic and rate performance. Mn-based oxides have received substantial attention as promising anode materials for LIBs due to their high theoretical specific capacities, low charge potential vs. Li/Li+, environmental benignity and natural abundance. Herein, the preparation of Mn-based oxide nanomaterials with various nanostructures and chemical compositions along with their applications as negative electrodes for LIBs are reviewed. The review covers MnO, Mn3O4, Mn2O3, MnO2, CoMn2O4, ZnMn2O4 and their carbonaceous composite/oxide supports with different morphologies and compositions. The aim of this review is to provide an in-depth and rational understanding of the relationships among the chemical compositions, morphologies and electrochemical properties of Mn-based anode materials and, to understand how electrochemical performance can be improved using materials engineering strategies. Special attention has been paid to the discussion of challenges in the practical applications of Mn-based oxides in LIB full cells.