A substrate processing method and a substrate processing system exclude wafers W provided with a protective film having surface defects that will cause components of a resist to dissolve in an immersion liquid during an immersion exposure process, and rated abnormal from those to be processed by the immersion exposure process. The substrate processing system is provided with a protective film forming module for forming a protective film on a resist film formed on a surface of a wafer W, an exposure system 4 for processing the surface of the wafer W coated with a transparent immersion liquid layer by an immersion exposure process, and a developing module 28 for processing the wafer W by a developing process using a developer. A protective film inspecting device 33 detects surface defects in a protective film formed on a wafer W. A control computer 60 decides whether or not surface defects detected by the protective film inspecting device 33 is normal on the basis of information about the surface defects provided by the protective film inspecting device 33, and gives a control signal representing the results of decision to the exposure system 4. The control computer 60 gives an exposure process execution signal requesting processing the wafer W by the exposure process to the exposure system 4 when the surface defects in the protective film are rated normal or gives an exposure process not executing signal requesting not processing the substrate by the exposure process to the exposure system when the surface defects in the protective film are rated abnormal.