The invention discloses a ground line selection method for a small current grounding system. The method solves the problem that the prior line selection method is low in sensitivity and generates errors in line selection. The method comprises the following steps: 1, single-circuit lines and double-circuit lines are numbered and placed in a microcomputer; 2, the microcomputer judges whether the system is grounded or not and identifies a grounding phrase of the system; 3, according to the number of the single-circuit lines and the double-circuit lines, the microcomputer calculates a grounding transfer characteristic formula with zero sequence current which is measured during the normal operation of the system, zero sequence current of the single-circuit lines, zero sequence voltage of a bus and zero sequence current of the double-circuit lines which are measured when the system is grounded, and zero sequence voltage of a bus, zero sequence current of the double-circuit lines and zero sequence current of the single-circuit lines which are measured during grounding transfer of the system; the result of the calculation is compared with grounding current IJ passing through a split phase switch of the grounding phase during grounding transfer to determine a fault line. The method has the advantages of the characteristics of high sensitivity and accurate line selection and great significance on accurate identification of grounding circuit, grasp of grounding and arc-suppression coil conditions of the system, and promotion and improvement of safe and reliable operation of the system.