Severe vibrations induced by flow instabilities in the nuclear reactor coolant pump (RCP) are detrimental to the safe operation of the pump. Due to the particular spherical casing in the RCP, the internal flow structures are extremely ambiguity and complicated. The goal of the present work is to shed comprehensive light on the unsteady flow structures and its correlation with the pressure pulsations by using large eddy simulation (LES) method of the RCP. The vorticity distribution and the shedding vortex from the blade trailing edge are depicted in detail. Furthermore, the internal correlations between the flow unsteadiness and pressure pulsation are illustrated in some special regions of the RCP. Evidently, some main excitation components in the pressure spectra are excited by the shedding vortex. Besides, components at blade passing frequency (fBPF) are closely associated with rotor–stator interaction between the wake flow from the impeller outlet and unsteadiness vortexes shedding from the diffuser blade trailing edge. It is thought to be that the pressure pulsations of the RCP are closely associated with the corresponding vorticity distribution and the unsteady vortex shedding effect.