According to one embodiment, a substrate processing system includes a measuring unit, a data processing unit, and a processing unit. The measuring unit is configured to measure information relating to a thickness dimension of a substrate. The substrate includes a light emitting unit and a wavelength conversion unit. The wavelength conversion unit includes a phosphor. The data processing unit is configured to determine processing information relating to a thickness direction of the wavelength conversion unit based on the measured information relating to the thickness dimension of the substrate and based on information relating to a characteristic of light emitted from the light emitting unit. The processing unit is configured to perform processing of the wavelength conversion unit based on the determined processing information.