Using a morpholino nucleotide wherein 5′-hydroxy group or a hydroxy group present on the substituent of the 5′-hydroxy group is protected by a protecting group having an alkyl group having not less than 10 and not more than 300 carbon atoms and/or an alkenyl group having not less than 10 and not more than 300 carbon atoms as a starting material, a method capable of efficiently producing the morpholino oligonucleotide in a high yield by a liquid phase synthesis can be provided.