Background: Chinese patent medicines are widely used in clinical practice, and their quality directly affects medication safety and therapeutic efficacy. The National Drug Sampling Inspection program serves as a critical quality surveillance mechanism. However, previous assessments have not systematically differentiated the risk levels of different non-conforming items, leading to potential risk misjudgment.Methods: This retrospective study analyzed inspection data of Chinese patent medicines from the National Drug Sampling Inspection conducted between 2020 and 2024. All inspection items were classified into appearance/description items and intrinsic quality test items. Risk stratification was performed across safety, efficacy, and stability dimensions.Results: Over five years, a total of 30,791 batches were inspected, with non-conforming rates of 0.54% (2020), 0.31% (2021), 0.65% (2022), 0.52% (2023), and 0.13% (2024). Identification, assay, related substances, dissolution, and microbial limits represented substantive high-risk defects. Description non-conformities, accounting for a minor proportion, predominantly involved minor appearance deviations that did not alter the intrinsic material basis. Risk stratification demonstrated clear differentiation between high-risk substantive defects and low-risk appearance deviations.Conclusions: Different inspection items correspond to markedly different quality risk levels. A risk-stratified regulatory approach is warranted to optimize regulatory resource allocation and improve the scientific basis of quality supervision for Chinese patent medicines.