LiMn2O4-based lithium-ion batteries (LIBs) have attracted considerable attention due to their cost advantage, but industrial use has been hindered by severe capacity deterioration during cycling with LiPF6-based carbonate electrolytes, especially under high-temperature (55 °C) cycling conditions. Herein, a bifunctional, Janus-faced, inorganic-organic hybrid separator is demonstrated to ensure long-term cycling reversibility of LiMn2O4||graphite LIBs. The monolithic all-nanomat separator is constructed by a bottom layer of poly (m-phenylene isophthalamide) nanofibers by electrospinning and a top layer of interpenetrating hydroxyapatite/bacterial cellulose fibers. Benefiting from such a unique Janus configuration, the as-formed separator exhibits synergistic coupling in functions, simultaneously scavenging trace acid and mitigating the dissolution/deposition of Mn2+ ions in batteries. Consequently, the cells with the Janus separator achieve enhanced capacity retention compared with traditional cells with the commercial polyolefin separator over 100 cycles at 55 °C. Furthermore, bulk structure and surface chemistry characterizations confirm that irreversible structural change in the LiMn2O4 cathode could be avoided, and the amount of manganese on the graphite anode from the cycled cells with the Janus separator is suppressed. This work demonstrates that a composite Janus all-nanomat separator offers an unexpected route towards highly durable LiMn2O4-based LIBs.