This study investigates the leakage vortex influence on pressure pulsation characteristics within a vertical axial flow pump. Three impeller configurations with blade root clearance (δ) of 2.7–8.0 mm were designed to analyze geometric effects on internal flow dynamics. Unsteady RANS simulations predicted flow structures under multiple operating conditions (0.8–1.2Q_des). Fast Fourier Transform (FFT) extracted frequency–domain and time–frequency characteristics of pressure pulsations in critical flow regions. Key results reveal: (1) δ enlargement expands low-pressure zones within blade channels due to enhanced leakage vortices; (2) leading-edge pulsation shows 8.2–11.7% reduction in peak-to-peak amplitude and fundamental frequency magnitude with increasing δ; (3) trailing-edge response exhibits non-monotonic behavior, with maximum amplitude at δ = 5.0 mm (42.2% increase at design flow). These findings demonstrate that blade root clearance optimization requires condition-dependent thresholds to balance leakage management and pulsation control.