A cleaning agent for a silicon wafer (a first cleaning agent) contains at least a water-based cleaning liquid and a water-repellent cleaning liquid for providing at least a recessed portion of an uneven pattern with water repellency during a cleaning process. The water-based cleaning liquid is a liquid in which a water-repellent compound having a reactive moiety chemically bondable to Si element in the silicon wafer and a hydrophobic group, and an organic solvent including at least an alcoholic solvent are mixed and contained. With this cleaning agent, the cleaning process which tends to induce a pattern collapse can be improved.