Affords a compound semiconductor substrate packaging method for preventing oxidation of the surface of compound semiconductor substrates. The compound semiconductor substrate packaging method provides: a first step of inserting a compound semiconductor substrate (10) into a gas-permeable, rigid container (20), placing the rigid container (20) into an inner-packing pouch (30) having an oxygen transmission rate of 1 to 100 ml·m−2·day−1·atm−1, and a moisture transmission rate of 1 to 15 g·m−2 ·day−1, replacing the air inside the inner-packing pouch (30) with an inert gas, and hermetically sealing the inner-packing pouch; and a second step of placing the sealed inner-packing pouch (30), and a deoxygenating/dehydrating agent (40) that at least either absorbs or adsorbs oxygen gas and moisture, into an outer-packing pouch (60) that has an oxygen transmission rate that is 5 ml·m−2·day−1·atm−1 or less and is lower than that of the inner-packing pouch (30), and a moisture transmission rate that is 3 g·m−2·day−1 or less and is lower than that of the inner-packing pouch (30), and hermetically sealing the outer-packing pouch (60).