A method for preparing a labeled sugar chain sample, comprising: diluting labeled sugar chains with a high-concentration organic solvent; applying the dilution to a silica-based carrier; washing the resulting carrier with a high-concentration organic solvent; and then subjecting the labeled sugar chains adsorbed on the carrier to elution with a water-containing solution. It has been found that this method makes it possible to remove substances other than labeled sugar chains efficiently with a remarkable reduction in the loss of labeled sugar chains (particularly labeled O-type sugar chains). Said substances other than labeled sugar chains include reagents, salts, additives, unlabeled substances, and so on.