The invention discloses an intelligent transformer substation relay protection test fault positioning method and system. The method comprises the steps that alarm information and data are preprocessed, repeated data are removed, and alarm information and the data which can be used for direct reasoning are removed from an original table and are stored separately; and fault positioning is performed,an existing template is used to carry out fault positioning on the alarm information and the data which can be used for direct reasoning, and for the alarm information and the data which need complexreasoning, parameters obtained by carrying out deep learning training by an RNN recurrent neural network are used to carry out fault positioning. In the invention, automatic positioning of relay protection test faults is realized, a fault processing speed is greatly improved, and test efficiency of a relay protection device is greatly increased.