To realize the detoxification treatment of the fluorine-containing waste residue from the production of an Al–Sc master alloy by molten salt electrolysis and recover valuable elements, based on the characteristics of a high fluoride and low scandium content in mineralogical compositions, the two-stage hydrometallurgical leaching of electrolytic slag from the Al–Sc alloy prepared by molten salt electrolysis was conducted for the recovery of fluorine and scandium. X-Ray diffraction (XRD), X-ray fluorescence (XRF), ion chromatograph (IC), inductively coupled plasma atomic emission spectrometer (ICP-OES), scanning electron microscope (SEM) were employed to investigate the trend and distribution of fluorine, scandium, and aluminum in detail. Results revealed that during the alkali leaching process, the fluorine in the molten salt slag was converted into sodium fluoride with low solubility, and almost all of the fluorine can be dissolved into the solution by washing with water. The scandium in the molten salt slag remained in the alkali leaching slag; therefore, the separation of fluorine and scandium was realized. By utilizing the insolubility of α-Al2O3 in less concentrated sulfuric acid at a low temperature, the alkali leaching slag was then leached by sulfuric acid to separate and recover scandium from α-Al2O3. Effects of the leaching agent concentration, liquid to solid ratio, leaching temperature, time, and other process parameters on the leaching rates in the alkali leaching and acid leaching processes were investigated. The optimum reaction conditions were determined to be a sodium hydroxide concentration of 100 g/L, a liquid to solid ratio of 12:1, a leaching temperature of 90℃, and a leaching time of 1.5 h for the alkali leaching process, and the sulfuric acid concentration of 1.5 mol/L, a liquid to solid ratio of 6:1, a leaching temperature of 90℃, and a leaching time of 50 min for the acid leaching process. Under the optimized parameters, the leaching rates of soluble aluminum and fluorine in the molten salt residue after alkali leaching were 97.12% and 98.71%, respectively. The purity of the sodium fluoride product reached 98.70%. Furthermore, the leaching rate of scandium reached 92.01% during the subsequent acid leaching process.