The invention relates to a deep sea ore lifting pump structure and a control method thereof, and belongs to the technical field of ore lifting pumps. The structure comprises an ore lifting pump shell;a high-speed shaft is arranged in the ore lifting pump shell; a flow separation driving mechanism is arranged between the high-speed shaft and the ore lifting pump shell; and a fine particle fluid channel is formed between the flow separation driving mechanism and the high-speed shaft, and is provided with multiple guide rotating impellers in limiting fixed sleeving with the high-speed shaft. Theflow separation driving mechanism comprises a low-speed rotating hub; a spiral blade disc is arranged on the outer wall of the low-speed rotating hub; and a speed reducer in limiting embedded fixation with the low-speed rotating hub is arranged in the low-speed rotating hub. The structure has the advantages of compact structure, good flow separation effect, good pulp passing performance, enough conveying power and long service life, can improve the conveying efficiency, can save axial space, realizes separate flowing of high-concentration large-particle pulp and fine-particle seawater to prevent the runner blockage phenomenon, and achieves the purposes of low wear of the pump by pulp in a runner and efficient flow passing.