The doctor–patient relationship has received widespread attention as a significant global issue affecting people’s livelihoods. In clinical practice within the medical field, applying existing artificial intelligence (AI) technology presents issues such as uncontrollability, inconsistency, and lack of self-explanation capabilities, even raising concerns about ethics and morality. To address the problem of doctor–patient interaction differences arising from the doctor–patient diagnosis and treatment, we collected the textual content of doctor–patient dialogues in outpatient clinics of local first-class hospitals. We utilized case scenario analysis, starting from two specific cases: multi-patient visits with the same doctor and multi-doctor interaction differences with the same patient. By capturing the external interactions and the internal thought processes, we unify the external expressions and internal subjective cognition in doctor–patient interactions into interactions between data, information, knowledge, wisdom, and purpose (DIKWP) models. We propose a DIKWP semantic model for the doctor–patient interactions on both sides, including a DIKWP content model and a DIKWP cognitive model, to achieve transparency throughout the entire doctor–patient interaction process. We semantically–bidirectionally map the diagnostic discrepancy space to DIKWP uncertainty and utilize a purpose-driven DIKWP semantic fusion transformation technique to disambiguate the uncertainty problem. Finally, we select four traditional methods for qualitative and quantitative comparison with our proposed method. The results show that our method performs better in content and uncertainty handling. Overall, our proposed DIKWP semantic model for doctor–patient interaction processing breaks through the uncertainty limitations of natural language semantics in terms of interpretability, enhancing the transparency and interpretability of the medical process. It will help bridge the cognitive gap between doctors and patients, easing medical disputes.