As a novel research model that can address multiple research questions within an overall trial structure, master protocol design shares similarities with the clinical research on syndrome-based traditional Chinese medicine in terms of study design. The sample size estimation in master protocol design is characterized by analyzing the subtrials separately and re-estimation at interim analyses. Specific methods include the combination of Simon’s two-stage design and Bayesian hierarchical design that facilitates information borrowing. By drawing on these methods to estimate dynamically and adjust the sample size for each subtrial in a targeted manner, it is expected to provide a feasible approach for the methodological development of sample size estimation in the field of clinical research on syndrome-based traditional Chinese medicine.