The invention relates to a high resistance grounding protection method and system for a low resistance grounding system. The high resistance grounding protection method for a low resistance grounding system includes the following steps: according to the value of a grounding fault transition resistor, presetting a zero sequence voltage condition, according to a zero sequence active power absolute value and the threshold value of the zero sequence active power absolute value, presetting a zero sequence active power absolute value condition, according to the relation between the zero sequence active power absolute value and the zero sequence reactive power absolute value, and presetting a zero sequence reactive power absolute value condition; and when the zero sequence voltage condition, the zero sequence active power absolute value condition and the zero sequence reactive power absolute value condition are satisfied at the same time, starting high resistance grounding protection for the low resistance grounding system. The high resistance grounding protection method for a low resistance grounding system can be adaptive to the polarity reversal connection situation of the special zero sequence CT, and does not need verifying the polarity of the special zero sequence CT.