The large differential protection of generator-transformer unit is one of the dual main protections. The traditional large differential protection of generator-transformer unit is easy to be influenced by current transformer saturation and the operation is slow. To dealing with above problems, a new criterion for large difference protection of generator-transformer unit based on improved Hausdorff Distance algorithm is proposed, which has high operation speed and anti-saturation capability. Firstly, the basic principle of the Hausdorff Distance algorithm is analyzed:when the fault occurs within the generator-transformer unit, the Hausdorff Distance constructed by the current of each terminal is big; when the fault is outside the generator-transformer unit or the system is under normal operation, the Hausdorff Distance constructed by the current of each terminal is smaller, which is basically 0. Based on this principle, a new criterion for the large difference protection of generator-transformer unit is proposed, and the threshold setting scheme is proposed. In addition, the current transformer saturation recognition strategy and protection opening strategy are proposed. Theoretical analysis and simulation results verify the effectiveness of the proposed protection scheme, which can quickly identify the internal fault and be reliably locked under external fault with current transformer saturation, can quickly open again under converted fault. The threshold value setting process is simple and not affected by system parameters. This work is supported by Science & Technology Program of Guangdong Power Grid Co., Ltd. (No. GDKJQQ20161176) and National Natural Science Foundation of China (No. 51677108).