Traditional Chinese medicine (TCM) formulas have a significant clinical efficacy, and the fingerprint technology has been widely accepted to fully reveal the quality of TCM. Whereas, it is a great challenge to establish the fingerprint chromatogram which can fully reflect every single herb material in a short time. In this study, we used Xiaojin capsule (XJC) as a case and developed a rapid fingerprint method based on increasing the column temperature and flow rate simultaneously combined with computer-aided. First, the elution gradient was optimized based on the retention parameters and peak shape parameters of the four linear gradients, and then, the column temperature and flow rate were increased simultaneously to shorten the analysis time. Next, the standard fingerprint chromatogram of XJC, which can reflect every herb material, was generated. Finally, quality markers were screened through unsupervised cluster analysis and supervised orthogonal partial least squares discrimination analysis. Combining computer-aided with increasing column temperature and flow rate simultaneously can develop the rapid method for establishing HPLC fingerprint of XJC, which can fully reflect every single herb material and provide comprehensive quality control. The strategy for establishing HPLC fingerprint of TCM formula could be applied to other traditional Chinese medicine formulas and herbal medicine.