we fabricate the black-silicon SERS substrate that is of high sensitivity to SERS signal and shows the proper intensity of the fluorescent background signal by plasma immersion ion implantation. Based on this substrate, the fluorescence peak shows a red-shifted phenomenon with the increase of concentration and their physical mechanism is explained. A good relationship between the position of fluorescence peak and the concentration of R6G is established with the coefficient of calibration plot being as high as 97.8%. Therefore, the substrate is used to determine the concentration of R6G based on the position of fluorescence peak. Different excitation power and accumulation time are performed and the results show that they have little effect on the position of fluorescence peak. In summary, the substrate would have a good potential in determining concentration of fluorescent contaminants due to the strong anti-interference ability as well as the fingerprint identification of SERS itself.