A system and a method for detecting a substrate and a manufacturing device are disclosed. The detection system includes: an emitting unit and a control unit; wherein the emitting unit provides a first reference light and a second reference light, the first reference light propagates to the control unit, the second reference light is modulated by the substrate to generate a test light, the test light propagates to the control unit; the control unit obtains and compares a power of the first reference light and a power of the test light so as to determine whether a foreign matter is present on a surface of the substrate. The detection system can prevent foreign matters such as photoresist from influencing other manufacturing devices such as cleaning and deposition devices, which is beneficial to the maintenance and service of the manufacturing devices.