The invention discloses a method for selectively clearing a single-phase ground fault of a ship shore power system. A variable reactor is arranged between a system neutral point and the ground. When the system is in a single-phase ground fault, the occurrence of the single-phase ground fault is judged according to the rise of a neutral point voltage to ground after the ship shore power system is in a single-phase ground fault; after the single-phase ground fault occurs, the variable reactor is controlled to act within the range of a time angle phi 0 in one cyclic wave of the changes of the neutral point voltage to ground, thus the variable reactor is controlled to gradually decrease a reactance value, and an instaneous tripping mechanism of a corresponding circuit breaker is triggered by gradually increasing short-circuit current so as to clear the fault, wherein the ranges of the time angle phi 0 are as follows: phi 0 is not smaller than 0 DEG and not larger than 50 DEG, phi 0 is notsmaller than 105 DEG and not larger than 230 DEG, and phi 0 is not smaller than 285 DEG and not larger than 360 DEG; and before the circuit is completely disconnected, a fuse connected with a corresponding position of the variable reactor is fused, so that the system is restored to a low-current grounding state and the ablation of a contact of a circuit breaker is avoided.