The natural flake graphite (GO) with an initial fixed carbon content of 6.23% is purified using flotation combined with alkali-melting acid leaching to obtain the high purity graphite (PG3) for energy storage. The graphite concentrate (PG1) with fixed carbon content of 85.62% is obtained by the selective enrichment of GO particles based on the multi-stage flotation. The alkali-melting acid leaching purification method is used to further purify the PG1 to obtain the PG3 with the fixed carbon content of 99.93%. The fixed carbon content is increased by 93.7% through flotation combined with alkali solution and acid leaching. The purification process of GO is systematically evaluated and analyzed by the several characterization techniques. The impurities removal mechanisms are also analyzed, which indicates that silicate and quartz in GO react with sodium hydroxide to form soluble substances, resulted in impurities removal. Oxide in GO and hydroxide formed in the alkali-melting process are subsequently removed in acid leaching process. The obtained PG3 could be used in lithium ion battery with a higher reversible capacity of 387 mAh g−1 compared to the 345 mAh g−1 of commercial layered graphite, which has promising potential application in energy storage. The above analysis indicates that the low purity GO is converted into high purify PG3 for energy storage, realizing high quality utilization of GO.