In order to overcome the disadvantage of low sensitivity of line selection method in neutral ineffectively grounded system when fault occurs near the zero-crossing point of phase voltage, a faulty line selection based on Hilbert transform is proposed, which carries out the wavelet packet decomposition of transient zero-sequence current for each line into low and high frequency subbands, whose instantaneous frequency are calculated by Hilbert transform at the same time, calculates the frequency band energy factors according to the wavelet coefficients. The frequency band energy factor is used as a condition of starting line selection method, when the high-frequency component is the main ingredient, we select the faulty line according to the maximum value of high-frequency wavelet energy; when the low-frequency component is the main ingredient, we select the faulty line according to the maximum value of DC component energy. A perfect scheme will be worked out combining with the two methods. Results of simulation show that, the proposed method, which is immune to the system structures and the mode of operations, has the characteristics of reliability, accurately and practicality.