The invention provides a transformer substation electric energy balance online control method capable of cooperative defect elimination. The method comprises the steps that an online balance centralized monitoring operation and maintenance system is built; an electric energy balance centralized monitoring group performs daily monitoring operation and maintenance on transformer substations of a whole province, finds non-balance exceptions timely, performs statistical analysis and launches a defect elimination procedure; a regulation and control center, a power transmission operation inspectiondepartment and a sales department transmit defect elimination information through work orders to achieve cooperative defect elimination. The method meets the requirement for the construction of a national power grid supporting network synchronous line loss system and is of great importance for deepening the construction of an electric quantity collection system, perfecting a balance monitoring andanalysis mechanism, improving the refined management level of an electric quantity system and improving the efficiency of cooperative operation and maintenance of dispatching, marketing, operation inspection and the like.