A method of manufacturing a substrate of a GaAs compound semiconductor is disclosed, which is characterized in that, after a crystal of GaAs compound semiconductor obtained by the liquid encapsulated Czocharalski method is annealed in the form of ingot, gradually cooled to room temperature and cut off in the form of a wafer, a re-heating treatment consisting of heating to a temperature of not lower than 700.degree. C., rapid cooling from the temperature of not lower than 700.degree. C. to a temperature of not higher than 400.degree. C. within 30 minutes and successive cooling to room temperature is given to the wafer, and then mirror polishing is performed.