The effect of different phase compensation methods on second harmonic ratio of magnetizing inrush is investigated. The flux linkage expression of switching on an unload transformer is deduced and influence factors of inrush current are analyzed firstly. Then the difference of two kinds of phase compensation methods, from star to delta and from delta to star connection, is compared. The second harmonic ratio of symmetric inrush is analyzed specially. Using inrush waveform of a real transformer, second harmonic ratio of phase inrush and that of differential current under two kinds of phase compensation methods are calculated respectively. Furthermore, based on the calculation results, the effect of two kinds of phase compensation methods on the inrush current identification is proved. The analysis and calculation results show that the second harmonic ratio of symmetric inrush caused by phase compensation method, from star to delta, is not low. Moreover, the split-phase blocking scheme should not be adopted for differential protection of from delta to star compensation. Using the phase current without compensation to calculate the ratio of second harmonic is inadvisable too.