The invention relates to a seed potato partitioning device and a partitioning method thereof, and belongs to the technical field of seed potato partitioning equipment. The seed potato partitioning device is characterized in that a conveying device is provided with a holding groove arranged along a conveying device; a carding plate (9), an image acquisition device and a jet flow cutting device (8)sequentially arranged along the conveying direction of the conveying device; the image acquisition device and the jet flow cutting device (8) are simultaneously connected with a control device; the jet flow cutting device (8) comprises a water jet scalpel nozzle (12) and a horizontal movement device; the water jet scalpel nozzle (12) is arranged downwards; and the horizontal movement device is connected with the water jet scalpel nozzle and pushes the water jet scalpel nozzle to horizontally move along the direction perpendicular to the conveying direction of the conveying device. According tothe seed potato partitioning device, seed potatoes can be cut through the jet flow cutting device according to bud eye information, and the virus cross-infection of the seed potatoes cannot be causedafter the seed potatoes are partitioned; and according to the partitioning method, the seed potato blocks are ensured to have 1 to 3 bud eyes, and the survival rate of seed potato blocks is ensured to be high.