A substrate processing method includes a substrate holding step of holding a substrate horizontally, a hydrophobic agent supplying step of supplying to an upper surface of the substrate a hydrophobic agent which is a liquid for hydrophobizing the upper surface of the substrate, a low surface-tension liquid supplying step of supplying the low surface-tension liquid to the upper surface of the substrate in order to replace the hydrophobic agent on the substrate by a low surface-tension liquid lower in surface tension than water, and a humidity adjusting step of adjusting humidity of the atmosphere in contact with a liquid film on the substrate such that the humidity of the atmosphere in contact with a liquid film on the substrate in the hydrophobic agent supplying step reaches a first humidity and the humidity of the atmosphere in contact with a liquid film on the substrate in the low surface-tension liquid supplying step reaches a second humidity which is humidity lower than the first humidity.