Aiming at the problem of notill seeding under conservation tillage conditions affected by the root-soil complex formed by corn stubble and soil, a corn stubble treatment mode of “row digging-extrusion crushing-vibration soil removal” was proposed, and a soil cleaning machine for corn stubble with row-digging was designed. It mainly consisted of double disc digging shovels, stubble conveying mechanism, concave plate-roller type root soil separation mechanism, shake type rod conveyor mechanism, etc. It can complete the digging, picking, root and soil separation of corn root-soil complex in one go. The structural design and kinematic analysis of its key components were conducted. The force and motion of the double disc digging shovel were analyzed, leading to the determination of its main structural and working parameters. The transportation and force conditions of the root-soil complex in each stage of root soil separation were analyzed, leading to the determination of main structural parameters and motion parameters of the stubble conveying mechanism, concave plate-roller type root soil separation mechanism and shake type rod conveyor mechanism. This ensured that the root-soil complex can gradually achieve the goal of root and soil separation. The field test results of the double disc digging shovel showed that the digging rate of the corn root-soil complex can reach 100%. The soil bin test results of the whole machine showed that the root and soil separation rate was 97.4%, and the root and soil separation rate was relatively high. The designed corn stubble digging and soil cleaning machine had effective stubble digging and root and soil separation capabilities.