To scientifically evaluate the quality risks of non-conforming Chinese patent medicines and establish a differentiated regulatory approach, this study is based on the inspection data of Chinese patent medicines from the National Drug Sampling Inspection conducted between 2020 and 2024. The distribution characteristics of non-conforming items were statistically analyzed, and risk-stratified assessment was performed by combining the results of routine testing and exploratory research. The results showed that the overall quality of Chinese patent medicines has maintained a steady upward trend. Identification, assay, related substances, dissolution, and microbial limits — as the core testing modules of pharmacopoeial standards — control the authenticity of the herbal prescription, the level of active pharmaceutical ingredients, impurity safety, in-vitro release behavior of the preparation, and microbial contamination risk, respectively. Non-conformity in any of the above items constitutes a substantive high-risk defect that may directly threaten medication safety and clinical efficacy. Some sampled products exhibited deviations in appearance and description without altering the intrinsic material basis of the medicines, posing a relatively low risk to actual clinical use. Quality hazards in Chinese patent medicines are mainly concentrated in inconsistent quality of Chinese herbal medicine raw materials, weak control over extraction and manufacturing processes, and enterprise quality control systems that exist in name only.