Fingerprint analysis is considered one of the most powerful approaches to quality control in traditional Chinese medicines (TCMs). In this study, a binary chromatographic fingerprint analysis was developed using hydrophilic interaction chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) to gain more chemical information about polar compounds and weakly polar compounds. This method was used to construct a chromatographic fingerprint of Ligusticum chuanxiong. The two chromatographic methods demonstrated good precision, reproducibility, and stability, with relative standard deviations of <2% for retention time and 7% for peak area for both HILIC and RPLC separations. Data from the analysis of 14 samples by HILIC and RPLC were processed with similarity analysis, with correlation coefficients and congruence coefficients. This binary fingerprint analysis, using two chromatographic modes, is a powerful tool for characterizing the quality of samples, and can be used for the comprehensive quality control of TCMs.