With the increasing demand for high-accuracy navigation, distributed payloads put forward higher requirements for the initial alignment accuracy of their equipped slave inertial navigation systems (INSs). However, the existing transfer alignment models have poor compensation effect on flexible deformation, resulting in low alignment accuracy. Moreover, these models cannot accurately evaluate the accuracy of transfer alignment due to ignoring the errors of the master INS. To address these two problems, a new high-accuracy transfer alignment system model is established by comprehensively considering errors of the master and slave INSs. Further, the propagation characteristics of the master and slave inertial sensor errors in transfer alignment are analyzed, and the relationship expression between the master and slave inertial sensor accuracy and the transfer alignment accuracy is derived. Thus, the accuracy of transfer alignment can be pre-evaluated according to the master and slave inertial sensor accuracy. The experiment results show that the alignment accuracy of the proposed method is improved by more than 71.56% compared with the traditional methods, and the relative errors between the proposed accuracy evaluation method and the Monte Carlo simulations are less than 9.14%. Thus, the correctness, effectiveness and superiority of the proposed method are verified.