Chinese patent medicines (CPM), generally prepared from several traditional Chinese medicines (TCMs) in accordance with specific process, are the typical delivery form of TCMs in Asia. To date, quality control of CPMs has typically focused on the evaluation of the final products using fingerprint technique and multi-components quantification, but rarely on monitoring the whole preparation process, which was considered to be more important to ensure the quality of CPMs. In this study, a novel and effective strategy labeling "retracing" way based on HPLC fingerprint and chemometric analysis was proposed with Shenkang injection (SKI) serving as an example to achieve the quality control of the whole preparation process. The chemical fingerprints were established initially and then analyzed by similarity, principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) to evaluate the quality and to explore discriminatory components. As a result, the holistic inconsistencies of ninety-three batches of SKIs were identified and five discriminatory components including emodic acid, gallic acid, caffeic acid, chrysophanol-O-glucoside, and p-coumaroyl-O-galloyl-glucose were labeled as the representative targets to explain the retracing strategy. Through analysis of the targets variation in the corresponding semi-products (ninety-three batches), intermediates (thirty-three batches), and the raw materials, successively, the origins of the discriminatory components were determined and some crucial influencing factors were proposed including the raw materials, the coextraction temperature, the sterilizing conditions, and so on. Meanwhile, a reference fingerprint was established and subsequently applied to the guidance of manufacturing. It was suggested that the production process should be standardized by taking the concentration of the discriminatory components as the diagnostic marker to ensure the stable and consistent quality for multi-batches of products. It is believed that the effective and practical strategy would play a critical role in the guidance of manufacturing and help improve the safety of the final products.