The invention provides a single-phase grounding protection method which is used for judging and isolating a single-phase grounding fault of a small-current grounding system. The single-phase grounding protection method comprises the following steps of: 102, synchronously acquiring the power frequency voltage of a bus of the small-current grounding system and current traveling waves of all outgoing lines corresponding to the bus in real time; 104, when the small-current grounding system is disturbed, determining a disturbance outgoing line according to the current traveling waves of all the outgoing lines; 106, determining whether the small-current grounding system has the single-phase grounding fault according to the power frequency voltage; and 108, determining that the disturbance outgoing line is a faulted outgoing line if the small-current grounding system has the single-phase grounding fault, sending a tripping instruction and insolating the faulted outgoing line. Correspondingly, the invention also provides a single-phase grounding protection system. By the single-phase grounding protection method and the single-phase grounding protection system, a requirement for judging the single-phase grounding fault of the small-current grounding system and a requirement for quick, reliable, sensitive and selective isolation can be met.