A substrate cleaning apparatus includes an indexer, a front surface cleaning unit for cleaning the front surface of a substrate, a back surface cleaning unit for cleaning the back surface of the substrate, a particle inspecting unit for detecting a distribution of particles adhering to the substrate, a reversing unit for reversing the substrate, and a transport section having a pair of transport units. Cleaning conditions of the front surface cleaning unit or back surface cleaning unit are varied based on the distribution of particles on the substrate after the substrate is cleaned by the front surface cleaning unit or back surface cleaning unit and inspected by the particle inspecting unit.