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It is important to marine ecology research that plankton samples are collected without damage, especially for time series samples. Usually, most fixed-point plankton samplers are made using a pump with paddle blades in order to increase the flow rate. But it can easily injure soft plankton. In this paper, a shaftless hollow sampling pump is designed, which can provide a highly efficient driving component for the plankton sampler. The numerical model of the sampling pump is established, and the flow rate of the sampling pump at different rotational speeds is simulated by the computational fluid dynamics method. In order to obtain a higher flow rate, the influence of internal and external cavity size, blade angle, and blade number on the flow rate of the sampling pump with a constant rotational speed of the blade was simulated and discussed. The results show that the flow rate at the internal cavity is positively correlated with the inlet and outlet pressure differences of the internal cavity, and the greater the negative pressure at the outlet of the internal cavity, the greater the flow rate. When the internal and external cavity sizes are h = 14 mm, d = 52 mm, blade angle θ = 45°, and number of blades s = 5, the flow rate of the sampling pump internal cavity reaches the maximum. Finally, the feasibility of the shaftless hollow sampling pump is verified by experiments. The shaftless hollow sampling pump can realize non-destructive sampling of plankton. This paper presents a theoretical design foundation for a new non-destructive siphon sampling method for marine plankton, which is of great significance for marine plankton sampling and subsequent research. Full article