The invention provides a compensation and apportion calculation method for a peak load regulation assisting service cost. The method comprises the steps of: firstly calculating a depth peak load regulation cost of a depth peak load regulation unit which includes a unit efficiency loss cost and an opportunity cost, and separately calculating the unit efficiency loss cost and the opportunity cost caused when the depth peak load regulation unit participates in peak load regulation assisting service; secondly, calculating compensation earnings of peak load regulation units and an apportion cost ofnon-peak load regulation units, and separately calculating the compensation earnings of thermal power peak load regulation units and the apportion cost of nuclear power units, wind power and solar energy power units and thermal power non-peak load regulation units failing to full the obligation of peak load regulation. The method achieves secondary reasonable allocation of costs and earnings, guarantees the economic benefits of units, realizes optimal configuration of peak load regulation resources and improves the peak load regulation capability of a power system.