A semiconductor device used for fluorescent-based molecule detection and a method for manufacturing the same are provided. The semiconductor device has a fluid channel layer defining a fluid channel through which a sample stream flows. A target cell coupled with a fluorescent source is contained by the sample stream. The semiconductor device also has an excitation light source for generating excitation light that reaches the target cell coupled with the fluorescent source to generate fluorescent light. The semiconductor device also has a light filter layer for permitting the fluorescent light to pass through and to block the excitation light and a light detection layer for detecting the fluorescent light. The functional components of the device are highly integrated. Leakage of the excitation light and background noise into the light detection component can be minimized to improve the quality of detection.