Basing on substructure analysis, original research on multi-stage model updating method (MSMUM) is presented to reduce the uncertainties in traditional model updating process. The kernel philosophy of the multi-stage model updating method is used to update a complicated FE model with multi steps, i. e. firstly localize the model errors and then update the error parameters. Comparing with the computed results, it is shown that the error localization methods and the parameter updating methods developed here are fine. As a case study, the model of the Runyang Nancha suspension bridge tower is updated with the MSMUM. Comparing the updated FE model here with the updated model using traditional updating method, it could be concluded that the multi-stage updating method is more effective.