The unsteady three‐dimensional numerical simulation calculation of the vertical axial flow pump device is performed based on CFD to examine the pressure pulsation and energy distribution features of the water flow within the siphon outlet conduit (SOC) under the hydraulic coupling of the pump and the flow conduit. The pressure pulsation signals (PPS) of monitoring points are decomposed using the Hilbert–Huang approach via empirical mode decomposition (EMD) and Hilbert spectrum analysis. The results show that the PPS of monitoring points of the SOC has no obvious periodicity. The low‐frequency range below 20 Hz serves as the primary frequency, and the energy ratio of the high‐frequency signal above 700 Hz is less than 1%. Under the condition of a small flow rate 0.3Qbep, there is obvious high‐frequency pulsation above 500 Hz at the inlet of the upstream section of the SOC, and there are periodic components distributed around 200 Hz. The energy of the pressure pulsation is primarily focused in the low‐frequency range below 40 Hz at the SOC outlet section. The PPS at the top and bottom monitoring points of the hump section are consistent, and the pressure pulsation energy (PPE) is mainly concentrated in the low frequency below 40 Hz. In both the big flow condition (1.2Qbep) and the optimal flow condition (1.0Qbep), the PPE of the monitoring points at the top of the hump section is distributed in the middle and low‐frequency band below 40 Hz, and the energy of monitoring points at the bottom of the hump section is concentrated in the low‐frequency band below 20 Hz, accounting for more than 70%. When the flow rate increases from 0.3Qbep to 1.2Qbep, the peak value of the pressure pulsation coefficient at the main frequency of each monitoring point at the top of the hump section changes little, and the peak value of the pressure pulsation coefficient at the main frequency of each monitoring point at the bottom increases first and then decreases. From the upstream section to the hump section of the SOC, the average frequency of each intrinsic mode function (IMF) of the PPS under different flow conditions shows an overall increasing trend. From the hump section of the SOC to its outlet, the average frequency of each IMF of the PPS decreases under the conditions of 1.0Qbep and 1.2Qbep, and there is no obvious change under the condition of 0.3Qbep.