In order to promote the application of Laser-Induced Breakdown Spectroscopy (LIBS) in the nuclear industry, in this paper, a femtosecond LIBS(fs-LIBS) system was used to quantitatively analyze Thorium (Th) in a highly pure graphite matrix. According to the Th concentrations in the Thorium-based fuel, a total of 9 homemade Th₂O₃-graphite mixture samples with Th concentrations that varied from 0.35% to 35.15% were prepared by the standard addition method. The favorable experimental parameters such as the treatment methods for LIBS detection, laser pulse energy and delay times were studied before the quantitative analysis. The results show that the signal intensity of the fs-LIBS spectrum acquired by the scanning with moving method is significantly higher than that without the moving method. For the Th I 396.21 nm line, the Relative Standard Deviation (RSD) value of multiple measurements for the scanning method was just 5.7%, which was much lower than that of without the moving method (20.4%). The Th spectral lines show obvious saturation due to the self-absorption effect in the higher concentration region, and thus the basic calibration method was no longer applicable. Therefore, an exponential function was used to fit the spectral line intensity and concentration in the whole concentration region, and the concentration saturation threshold values corresponding to the analytical lines Th I 394.42, 396.21, and 766.53 nm were obtained. The basic calibration method has good detection performance when the calibration curves were constructed by using a lower concentration below the saturation threshold. For the peak area and peak intensity of each analytical line, using the internal standard method with the internal standard line (C I 247.85 nm), a good linear relationship can be found between them and the Th concentrations in the whole concentration region, especially for analytical line Th I 766.53 nm with a higher saturation threshold. The internal standard method had good prediction performance for unknown samples with higher concentrations. The above results show that fs-LIBS has the potential to monitor and analyze the thorium concentration in the thorium-based fuel cycle.