The flow field structure within the clearances of turbomachinery is complex and diverse, exhibiting high-dimensional nonlinearity. How to accurately extract the main structures that affect the internal flow within the turbine from the complex clearance flow has always been a key issue. To explore the impact of the dynamic structure of the clearance flow on the mainstream region in a centrifugal pump, this study combines the dynamic mode decomposition (DMD) method to conduct a thorough analysis of the velocity and pressure pulsation frequencies in the multi-physics fields within the clearance. The study has identified the main characteristic structures under different physical conditions in the clearance and has established the relationship between the characteristic structure frequencies in different physical fields and the impeller frequency. The research indicates that the internal flow within the clearance affects the occurrence of vortices in the volute. Under design conditions, the velocity field within the clearance is primarily influenced by high-order harmonic frequencies of the impeller, and the pressure field is mainly affected by low-order harmonic frequencies of the impeller. This reflects the crucial influence of impeller frequency and inlet flow on the coherent structures within the clearance flow. The research results offer new insights and methods for analyzing complex internal flows in large turbomachinery.