The invention provides an automatic transplanting machine for plug seedlings and a control system thereof. The automatic transplanting machine for plug seedlings comprises a chassis, a moving box mechanism, a seedling-picking mechanism, a seedling-separating mechanism, a seedling-transplanting mechanism and a power mechanism. The moving box mechanism, the seedling-picking mechanism and the seedling-separating mechanism are fixed on the chassis in sequence from front to back; the seedling-transplanting mechanism is arranged below the seedling-separating mechanism to be connected with the chassis, and the seedlings dropped from the seedling-separating mechanism can accurately enter the seedling-transplanting mechanism. Seedling feeding, seedling picking, seedling separating, seedling dropping and seedling transplanting can be conducted at high speed by respective mechanism under the coordination of an automatic seedling feeding control system, an automatic seedling picking control system and an automatic seedling throwing control system. The automatic transplanting machine for the plug seedlings has simple mechanical structure and low cost; input signals required by the control system are less, control method is simple, flexible and efficient, and the automatic transplanting machine for the plug seedlings is thus suitable for a high speed transplanting operation.