Medical group conflict decision making is one of the dominant research problems in the field of group consensus decision making. We base the research background on the optimization of clinical diagnosis and treatment in the traditional Chinese medicine (TCM) and Western medicine, and propose a novel multi-granularity sequential three-way group conflict decision with preference degree regarding the increment of decision makers and the conflicting characteristics of the decision group. Firstly, we construct a 19-scale multi-granularity conflict preference information system, and then build a generalized conflict decision making granular computing model over this 19-scale conflict information system. Secondly, we establish a sequential three-way group conflict decision making method based on the generalized conflict decision making granular computing model. Furthermore, we define three forms of group conflict result. Meanwhile, we give the definition of preference degree, represent a quantitative presentation of the diagnosis and treatment of rheumatoid arthritis (RA) in TCM and Western medicine, conclude trisection result of preference aggregation of each level group, and design an algorithm of multi-granularity sequential three-way group conflict decisions model with preference degree. Thirdly, we apply the proposed model to an example of the clinical decision-making process of TCM and Western medicine. In addition, this paper also presents the following application work, on the one hand, we verified the validity, applicability, and scientificity of the multi-granularity sequential three-way group conflict model. On the other hand, subjective knowledge is quantitatively characterized by an abstract theoretical model, which is scientific significance of the optimization of clinical diagnosis and treatment schemes for such similar diseases, and the weakening or elimination of the conflict between traditional Chinese medicine (TCM) and Western medicine, and the deep integration of TCM and Western medicine. Finally, the research can provide an innovative way of thinking for the development of internationalization and standardization of TCM.