The invention discloses a method and system for judging an excessively great energy supply flow difference value. The method comprises that judgment is carried out on any data independently collectedby a main station of an energy measurement management system in allusion to all branch lines of the same energy transmission main line. The energy supply flow difference is determined to be too greatin the following conditions: the energy supply flow values of all branch line measurement equipment are greater than 0 and not less than 6 times of the standard energy supply flow value; the difference between the maximum value and the minimum value of the energy supply flow of each set of branch line measurement equipment is calculated, and the difference value between the maximum value and the minimum value of the energy supply flow of each set of branch line measurement equipment is obtained, and the ratio between the difference value and the maximum value of the energy supply flow of eachset of branch line measurement equipment is greater than a threshold of the measurement equipment; and the energy supply flow values of all branch line measurement equipment are less than 5% of the standard energy supply flow value, or the energy supply flow values of all branch line measurement equipment are not less than 0.5% of the standard energy supply flow value.