The molecular structure of polymer precursors significantly affects their rheological properties, thermal stability, and ceramic conversion rates. For the first time, we revealed the effects of polyborazane molecular structure on rheology and molecular configuration dynamic transformation process. The systems studied are polyborazane precursors with rigid six‐membered ring structures. We synthesized precursors with different molecular structures, including polyborazanes with varying degrees of branching and molecular chain flexibility, and investigated how molecular structure affects viscosity under different conditions of temperature, time, and shear rates. The results indicate that decreasing the branching degree enhances thermal stability and reduces both zero‐shear viscosity and infinite‐shear viscosity. Increasing the flexibility of molecular chains notably reduces infinite‐shear viscosity, while having minimal impact on zero‐shear viscosity and thermal stability. In conclusion, the ideal molecular structure should aim to increase the flexibility of the molecular chains while maintaining a certain degree of branching, such as a dendritic molecular configuration. By correlating viscosity data with molecular structure, we constructed a dynamic transition process of molecular chain entanglement, disentanglement, and crosslinking. This research is essential for understanding polymer rheology and its applications in industry, particularly in designing and synthesizing precursor structures for producing various ceramic fibers through Polymer‐Derived Ceramics.