A method of cleaning a substrate having a metal layer including copper or a copper-containing alloy, the method including cleaning the substrate using a cleaning liquid that includes a mercapto compound represented by one or both of the following formulas (1) and (2), and a solvent containing water and a water-soluble organic solvent: in which R represents a substituent group; m is an integer of 1 to 3; and n is an integer of 0 to 3, when m is 2 or 3, R may be the same or different; HS—(CH2)x—OH  (2), in which x is an integer of no less than 3.