The invention relates to a synthesis method of 6''-N-ethyl gentamicin C1a. The synthesis method of the 6''-N-ethyl gentamicin C1a comprises the following steps that (1) a compound 1 gentamicin C1a isdissolved in a solvent for cooling, BOC-ON is added and stirred, and water and ethyl acetate are added to be subjected to liquid separating, water phase taking, and condensing to obtain a compound 2;(2) a concentrated solution is dissolved by methanol, triethylamine is added for cooling, and acetic anhydride is added, stirred and condensed to remove a solvent; (3) hydrochloric acid is added to aconcentrated solution, and stirred at the room temperature, pH is adjusted by a sodium hydroxide solution for concentration, and a compound 3, namely 1,3,2''-N,N,N-triacetyl gentamicin C1a is obtainedby purification and separation through a silica gel column; and (4) after the 1,3,2''-N,N,N-tracetyl gentamicin C1a, glycol dimethyl ether, hexamethyldisilazane and a concentrated sulfuric acid are mixed and heated until refluxing and dissolving, stirring and concentrating continue to be conducted to remove the solvent so as to obtain a compound 4, dichloromethane is added for cooling, acetaldehyde is added to be stirred, potassium borohydride is added to be stirred, a borate buffer solution is added to be stirred, sodium hydroxide is added for condensing and removing the dichloromethane, thesodium hydroxide is added for heating and refluxing, and macroporous resin is subjected to desalination and separation to obtain a compound 5, namely 6''-N- ethyl gentamicin C1a.