Recycling and reusing the Waste carbon residue (WCR) from spent lithium-ion batteries has substantial significance in environmental protection and economic growth. Nevertheless, research on the regeneration of WCR was seldom reported. Herein, a new environmentally friendly process of low-temperature fluorination roasting and water leaching technology were proposed to achieve optimal purification of WCR. And the transformation mechanism of water-soluble complex ions during fluorination roasting was investigated via DFTB indicating that the ionic bond of F and NH4 group in NH4F broken than form stable covalent bond with metal ions. This process showed that 99.59%, 99.54%, 99.82%, 96.38%, 98.41%, 97.28%, 99.23%, and 98.61% of cobalt, nickel, manganese, aluminum, silicon, iron, lithium, and sulfur in WCR could be removed under optimal conditions. Meanwhile, the high-Purity graphite carbon (PGC) products with purity of 99.98% were obtained. In particular, PGC in half-cell exhibited a stable specific capacity of 340.9 mAh/g and high ICE of 92.13%, and with a more than 96% capacity retention after 100 cycles at 1C, much better performance than WCR and similarly to commercial graphite. Moreover, the discharge capacity of PGC in full-cell was 2302.82 mAh at 0.2C rate with 87.3% ICE. The capacity retention maintained at 96% after 400 cycles at 1C/1C rate. Subsequently, the valuable components in leaching solution were recovered with ammonia as precipitant. The precipitation rates of Al, Co, Mn, Ni, and Si were 99.25%, 81.74%, 98.20%, 62.43% and 86.68%, respectively. Besides, exhaust gas was absorbed in fluorine-containing leachate for recovery of ammonium fluoride products by evaporation crystallization. This proposed process with circular economy and green chemistry characteristics is expected to be employed in the regeneration of WCR while recovering valuable components.