The performance of the transfer alignment has great impact on inertial navigation systems. As the transfer alignment is generally implemented using a filter to compensate the errors, its accuracy, rapidity and anti-disturbance capability are key properties to evaluate the filtering process. In terms of the superiority in dealing with the noise, H∞ filtering has been used to improve the anti-disturbance capability of the transfer alignment. However, there is still a need to incorporate system uncertainty due to various dynamic conditions. Based on the structural value theory, a robustness stability analysis method has been proposed for the transfer alignment to evaluate the impact of uncertainty on the navigation system. The mathematical derivation has been elaborated in this paper, and the simulation has been carried out to verify the effectiveness of the algorithm.