Diagnostic errors represent a critical issue in clinical diagnosis and treatment. In China, the rate of misdiagnosis in clinical diagnostics is approximately 27.8%. By comparison, in the United States, which boasts the most developed medical resources globally, the average rate of misdiagnosis is estimated to be 11.1%. It is estimated that annually, approximately 795,000 Americans die or suffer permanent disabilities due to diagnostic errors, a significant portion of which can be attributed to physicians’ failure to make accurate clinical diagnoses based on patients’ clinical presentations. Differential diagnosis, as an indispensable step in the clinical diagnostic process, plays a crucial role. Accurately excluding differential diagnoses that are similar to the patient’s clinical manifestations is key to ensuring correct diagnosis and treatment. Most current research focuses on assigning accurate diagnoses for specific diseases, but studies providing reasonable differential diagnostic assistance to physicians are scarce. This study introduces a novel solution specifically designed for this scenario, employing machine learning techniques distinct from conventional approaches. We develop a differential diagnosis recommendation computation method for clinical evidence-based medicine, based on interpretable representations and a visualized computational workflow. This method allows for the utilization of historical data in modeling and recommends differential diagnoses to be considered alongside the primary diagnosis for clinicians. This is achieved by inputting the patient’s clinical manifestations and presenting the analysis results through an intuitive visualization. It can assist less experienced doctors and those in areas with limited medical resources during the clinical diagnostic process. Researchers discuss the effective experimental results obtained from a subset of general medical records collected at Shengjing Hospital under the premise of ensuring data quality, security, and privacy. This discussion highlights the importance of addressing these issues for successful implementation of data-driven differential diagnosis recommendations in clinical practice. This study is of significant value to researchers and practitioners seeking to improve the efficiency and accuracy of differential diagnoses in clinical diagnostics using data analysis.