The present invention relates to a deviation electric quantity settlement method, which comprises steps of performing a peak, flat and valley time division on an electricity purchasing and selling area according to a load level in the electricity purchasing and selling area; respectively determining deviation electric quantity reference electricity prices of the peak, flat, valley periods in the electricity purchasing and selling area; using the relation between an electricity purchasing/selling contract electricity price and the deviation electric quantity reference electricity price to determine a settlement electricity price of the deviation electric quantity of an electricity purchasing/selling contract; and determining settlement electricity charge of the electricity purchasing/selling contract according to the settlement electricity price of the deviation electric quantity of the electricity purchasing/selling contract. The method provided by the invention gives the real-time price attribute of the deviation electric quantity. Under the framework of the trans-regional and trans-provincial power transaction which has not established the real-time market temporarily, the specific real-time pricing method is used for preventing transaction participants from using the deviation electric quantity arbitrage to disorder the market, enhances the binding of the transaction contract, plays the role of optimal scheduling, and does not exorbitantly increase the complexity of the pricing and settlement work system, and has a strong practical value.