The invention discloses an electrical separation hierarchical topology analysis method for a transformer substation. The method comprises the following steps: (1) classifying primary equipment of the transformer substation according to hierarchical structures of a transformer winding, a busbar group and electrical separation; (2) under a condition that the topology busbar group includes two busbars, identifying 3/2 structural wiring in the electrical separation according to the number o switches, and identifying relevant equipment subjected to the 3/2 structural wiring according to a wiring mode; and (3) under a condition that the topology busbar group includes a single busbar, identifying internal bridge structural wiring in the electrical separation according to the number of switches and the type of the switches, and identifying relevant equipment subjected to the internal bridge structural wiring according to the wiring mode. According to the electrical separation hierarchical topology analysis method for the transformer substation, primary main wiring equipment of the transformer substation is classified according to the hierarchical structures of the transformer winding, the busbar group and the electrical separation, so that the connection relationship among the equipment is better in sense of organization and intuition, the topology requirement in advanced applications such as fault diagnosis and separation state analysis is met more conveniently, and the flexibility is improved.