Configuration optimization method of transformer magnetic bias treatment is proposed on the basis of multi-index comprehensive evaluation. First, based on the analysis of the mechanism of transformer magnetic bias and its influence factors, this paper constructs a satisfactory optimization model. Followed, satisfaction degree and urgency of each substation influenced on transformer magnetic bias is calculated. Then the minimal set of substations that need to be treatment is selected by iterative algorithm. Finally, an example is given and the application effect of configuration optimization method is also summarized. With the applying of the configuration optimization method, the treatment devices of transformer magnetic bias can be rational distribution, and the control area by single treatment device can be extended. Moreover, equipment utilization can be improved and the investment of treatment device can be reduced.