The present invention relates to a sensor chip for biomedical and micro-nano structured substances and a method for manufacturing the same. The sensor chip includes plural metal nanoparticles and a porous anodized aluminum oxide film. The plural metal nanoparticles are completely contained in holes of the porous anodized aluminum oxide film and located at the bottom of the holes, and an aluminum oxide layer covering the second end of the holes has a thickness of 1 nm to 300 nm. When analytes such as biomedical molecules are provided in contact with the sensor chip, a Raman signal can be detected based on the Raman spectroscopy. The structure of the sensor chip of the present invention is uncomplicated and the manufacturing steps thereof are simple, and therefore the sensor chip of the present invention is of great commercial value. Also, a method of manufacturing the above sensor chip is disclosed.