In this paper, for some special short-circuit faults of transformers, such as balancing winding fault and through faults between primary-side and secondary-side, the method of transformer internal faults locating caused by out-of-zone faults is studied by using the characteristics of transformer voltage, current and differential current. Based on the transient fault recorder data of transformer relay protection, theory analysis and calculation is implemented. The fault location and type are identified gradually by utilizing the reasoning and exclusion method. Finally, the fault condition is determined. It shows that the transformer relay protection tripped correctly in these faults by simulation and checking in field. More, the progress of this fault investigation and location is introduced, which is benefit to primary equipment inspection and deal with fault condition.