Biomass energy (such as biogas) has been one of the most important ways to reduce greenhouse gas emission during the economic transformation of China. It is necessary to carefully treat the transporting of biogas mixture, due to its high risk in rural areas, where there are extensive biogas projects. Particularly, a gas-liquid multiphase pump can be required higher stability during transportation. The condition of low discharge can be attributed to the unstable region of the pumps. In this case, the vibration of the pump can be aggravated to sharply deteriorate the stability of the pump. In severe cases, it may even cause damage to the components of the multiphase pumps. Therefore, it is highly urgent to clarify the influence of various factors on the vibration in the multiphase pumps under low discharge. Among them, a Gas Volume Fraction (GVF) is an important parameter in the operation of gas-liquid multiphase pumps. Taking a three-stage mixed-flow multiphase pump as the research object, this study aims to establish a multi-channel vibration test system, further to collect the vibration signals of the shaft and bearing, when transporting the liquid with different GVF at low discharge. The vibration signal processing was conducted to determine the influence of the GVF on the vibration of the shaft and bearing house. The results showed that the peak-to-peak value for the radial vibration of the shaft first increased and then decreased, with the increase of the GVF, indicating an outstanding nonlinear behavior. The radial vibration amplitude of the shaft caused by the increase of GVF reached 3.2 times that at pure water conditions. Besides, the increasing GVF mainly dominated the axial vibration of the bearing house, indicating a small effect on the radial vibration. The axial vibration amplitude of the bearing house was greater than the radial vibration at all working conditions. The amplitude frequency of the shaft radial vibration was attributed to the transition conversion of the gas-liquid two-phase flow pattern in the multiphase pump. Once the GVF increased from low to high, the two-phase flow pattern was changed from the bubble flow to the gas pocket flow in the multiphase pump. The local congestion in the pump inlet tee was induced the significant low-frequency components in the frequency spectrum for radial vibration of the shaft. The increasing GVF also presented a certain strengthening effect on the rotor-stator interaction between the impeller outlet and the guide vane inlet. In the range of (0-20%) GVF, the peak value of the Probability Density Function (PDF) for the radial vibration of the shaft decreased, with the increasing of the GVF. Once the GVF exceeded 20%, the peak value of the PDF increased in the radial vibration of the shaft, as the GVF increased, indicating two opposite trends. The finding can also provide a strong reference to evaluate the GVF in the mixed-flow pumps.