The limited penetration of photons in biological tissue restricts the deep-tissue detection and imaging application. The micro-scale spatially offset Raman spectroscopy (micro-SORS) with an optical fiber probe, colleting photons from deeper regions by offsetting the position of laser excitation from the collection optics in a range of hundreds of microns, shows great potential to be integrated with endoscopy for inside-body noninvasive detection by circumventing this restriction, particularly with the combination of surface-enhanced Raman spectroscopy (SERS). However, a detailed tissue penetration study of micro-SORS in combination with SERS is still lacking. Herein, we compared the signal decay of enhanced Raman nanotags through the tissue phantom of agarose gel and the biological tissue of porcine muscle in the near-infrared (NIR) region using a portable Raman spectrometer with a micro-SORS probe (2.1 mm in diameter) and a conventional hand-held probe (9.7mm in diameter). Two kinds of Raman nanotags were prepared from gold nanorods decorated with the nonresonant (4-nitrobenzenethiol) or resonant Raman reporter molecules (IR-780 iodide). The SERS measurements show that the penetration depths of two Raman nanotags are both over 2 cm in agarose gel and 3 mm in porcine muscle. The depth could be improved to over 4 cm in agarose gel and 5mm in porcine tissue when using the micro-SORS system. This demonstrates the superiority of optical-fiber micro-SORS system over the conventional Raman detection for the detection of nanotags in deeper layers in the turbid medium and biological tissue, offering the possibility of combining the micro-SORS technique with SERS for noninvasive in vivo endoscopy-integrated clinical application.