The assembly of two different materials into a composite with binary superlattices can provide a most efficient and inexpensive path to the synthesis of electrode materials with high energy density. Here, Li9Fe3P8O29/Na2HPO4 binary superlattice ceramic membrane-coated mesoporous soft carbon/hard carbon microspheres (BSLCM-MSC/HCMs) are synthesized via a hydrothermal carbonization method using acyl nucleoside triphosphate disodium salt (Na2ATP) as a multifunctional template. Here Na2ATP is not only a phosphorus source, a sodium source and a nucleating agent for the rapid synthesis of BSLCM, but also is a carbon source which is easily transformed into MSC/HCMs after being heat-treated in a N2 atmosphere. This special structure design brings a remarkable synergic effect for both Li+/Na+ mixed-ion storage and transfer kinetics. As a new nanocomposite cathode for mixed-ion batteries (MIBs), the BSLCM-MSC/HCMs display a self-enhancement of discharge capacity via electrolyte penetration in the core-shell mesoporous microspheres. Importantly, the discharge specific energy of a MIB assembled with the BSLCM-MSC/HCMs-2 cathode is up to 400 W h kg−1 at a high current rate of 10C, which outperforms all lithium-ion batteries and sodium-ion batteries reported so far. The findings in this study may benefit to the development of high energy mixed-ion batteries.