To provide a method capable of simply optimizing an elution condition, to simplify a process, to shorten days for the process and to automatize the process in a high-purity purification method for an oligonucleotide by a conventional liquid chromatography.

In this two-stage purification method for an oligonucleotide comprising (a) a process for purifying a synthetic oligonucleotide containing a hydroxyl group protected with a hydrophobic protecting group by a liquid chromatography, (b) a process for deprotecting the hydrophobic protecting group of the purified oligonucleotide and (c) a process for purifying the deprotected oligonucleotide by a liquid chromatography, the collections of the oligonucleotide in the processes (a) and c are carried out by responding the detections of the absorbances of eluted solutions of liquid chromatography reaching a fixed value or higher than it by a detector.