The invention discloses a method and system for controlling the capacity of transformer substations of an initiative power distribution network. On one hand, the uncertainty of loads is considered, and the power distribution network dispatching participating degrees of the loads in total loads of the power distribution network are analyzed; on the other hand, contribution conditions of distributed energy resources in the power distribution network are considered, trusted contribution values of the distributed energy resources in the power distribution network are calculated, the total capacity of the transformer substations in the planned year is calculated according to the maximum load predicated value of the power distribution network and the trusted contribution values of the distributed energy resources in the power distribution network, and the capacity of the transformer substations of the power distribution network is further controlled according to the total capacity of the transformer substations in the planned year. In the whole process, the uncertainty of the loads and the contribution conditions of the distributed energy resources are sufficiently considered, the accuracy of the calculating result of the total capacity of the transformer substations in the planned year is guaranteed, the capacity of the transformer substations of the power distribution network can be accordingly and accurately controlled, and effective use of the resources and safe operation of the power distribution network are guaranteed.