Rhizoma Atractylodis Macrocephalae (RAM) is a commonly used food and traditional Chinese medicine (TCM), which traditionally strengthens the spleen, benefits vital energy, eliminates dampness, and promotes hidroschesis. Its primary effective constituents are polysaccharides and volatile oil, whose main components are atractylenolide I and III. Fourier transform near-infrared spectroscopy (FT-NIR) is widely used in TCM research. However, determination of atractylenolides in RAM using FT-NIR has not been described. In this study, a new method for the determination of atractylenolides I and III in RAM by NIR was established. The spectral characteristics of atractylenolides I and III were obtained by second derivative multiple scattering correction, and its chart to the original absorbance spectra. Additionally, in combination with the partial least squares (PLS) algorithm, the calibration process was performed for the quantitation of the samples. The root mean square error of cross-validation of the PLS models for atractylenolides I and III was 0.0387 and 0.0358, and the determination coefficient of quantitative models was 96.63 and 96.16, respectively. This study demonstrated that NIR spectroscopy can be used to analyze quickly and efficiently the contents of atractylenolides I and III in RAM.