A method of manufacturing an optical semiconductor apparatus includes: placing a light transmissive lid body on a package substrate adapted to house an optical semiconductor device in an atmosphere of a first gas containing oxygen (O2), sandwiching a bonding member containing gold-tin (AuSn); exchanging an atmosphere gas for a second gas so as to reduce an oxygen concentration in the atmosphere while a load is exerted from above the lid body placed on the package substrate for temporary sealing; and heating and melting the bonding member after an exchange for the second gas is started so as to bond the package substrate and the lid body.