The invention discloses a control method and system for converting a paralleling operation into a separated operation for a dual-bus section substation. The switching between the paralleling operation and the separated operation is performed by only obtaining states of switches according to a switching instruction and the switch states without requiring a manual operation and intervention judgment of an operator; the separated operation of the bus is restored; the operation safety can be ensured, and the operation time is shortened; the power outage time of a client is reduced to the minimum, and the index requirements on safety and reliability are satisfied; a bus-coupler switch is switched off firstly and then a main transformer switch is closed, so that a condition of switch fault explosion can be effectively avoided in a substation with out-of-limit short circuits, and the power supply safety is ensured.