The poor compatibility between dimethyl methylphosphonate (DMMP)-based electrolytes and carbonaceous anodes was improved by optimizing the compositions of the electrolyte and the electrode. In the electrolyte, the contents of DMMP and ethylene carbonate had significant effects on both the safety characteristic and the compatibility with carbonaceous anode. For the spherical mesocarbon microbeads, a conductive composite system containing the flake graphite and the carbon nanoparticles was beneficial to the highest reversible capacity (330 mAh g−1). In the common graphite anode, the water-soluble binder was the better choice than poly(vinylidene fluoride) to suppress the reductive decomposition of DMMP. In brief, the optimized compatibility indicated an extensive prospect of the flame-retarded electrolyte in the battery industry.