A method for efficiently purifying 5 protected 2-deoxypurine nucleosides, efficient production of which has previously been difficult. Impurities can be separated by obtaining the 5 protected 2-deoxypurine nucleoside as an inclusion crystal including a solvent such as that having a nitrile structure in order to purify the 5 protected 2-deoxypurine nucleoside at a high purity. This invention enables synthesis of highly purified protected deoxypurine nucleosides easily on a large scale, which has previously been performed by column chromatography method.