The hydrodynamic and sediment movement of MP6-R micro-magnetic pump under three inlet flow rates(0.5, 1.0, 1.5 m/s) and three sediment concentrations(0.5%, 1.0%, 2.0%) were numerically simulated by the method of computational fluid dynamics coupled with discrete element method. The results show that when the inlet flow rate is 0.5 m/s, a backflow zone with the maximum backflow velocity of 1.07 m/s appears in the interface section between the outlet pipeline and the volute of the magnetic pump. With the increase of the inlet flow rate, the backflow velocity gradually decreases. When the inlet flow rate reaches 1.5 m/s, the backflow phenomenon disappears, and the magnetic pump has the best flow performance with the stable flow velocity direction pointing to the outlet. There are a large number of retention areas where low velocity sand particles converge near the axial surface of blade wheel. When the inlet velocity is constant, the change of particle volume fraction has little effect on the average velocity of sand particles in the retention area. When the inlet flow rate was lower than 1.0 m/s, the increase of the particle volume fraction significantly reduced the particle residual ratio, but when the inlet flow rate was higher than 1.0 m/s, the particle volume fraction was very close. When the volume fraction of particles is constant, increasing the inlet velocity decreases the particle residual ratio and increases the average velocity of sand particles in the stagnant area. When the inlet velocity reaches 1.0 m/s, the particle residual ratio and the average velocity of sand particles in the stagnant area do not change significantly with the inlet velocity, and the magnetic pump has the best transport performance. The maximum pressure and the area on the high pressure surface of the impeller can be reduced by increasing the inlet velocity, which led to the lower load intensity on the impeller surface. Considering the overflow performance, conveying performance and the load intensity of the impeller surface, it is suggested that the inlet flow rate of the magnetic pump should be kept above 1.0 m/s under the optimal running state.