The invention discloses a bus disconnecting link position detection method in a thermal inverted bus process based on a main station system and a system thereof. The method comprises the following steps of receiving a remote communication displacement signal of a bus disconnecting link, wherein the signal is sent by a power plant or a transformer substation; if multiple groups of thermal inverted bus equipment combinations which are prestored have a thermal inverted bus equipment combination including the bus disconnecting link, taking the thermal inverted bus equipment combination including the bus disconnecting link as an equipment combination to be measured; determining whether active power parameters of each equipment in the equipment combination to be measured which is acquired in advance satisfy a preset requirement in a preset time period before a moment of receiving the remote communication displacement signal, if the parameters satisfy the preset requirement, after preset time is delayed from the moment of receiving the remote communication displacement signal, acquiring and determining whether active power balance amounts of two buses in the equipment combination to be measured are greater than a preset balance threshold respectively, and if the active power balance amounts are not greater than the preset balance threshold, sending a first alarm signal to an alarm system so as to give an alarm. In the invention, whether the bus disconnecting link is closed in place during a thermal inverted bus process in the power plant or the transformer substation can be detected and the alarm can be given out, and reliability is high.