In this paper, in-flight alignment algorithm using UKF is presented for an SDINS aided by SSBL or GPS system under large initial heading error. The EKF usually applied for this task. This approximates the propagation of mean and covariance accurate to first-order only. To overcome this limitation, the unscented transformation that achieves second order approximation is applied to the in-flight alignment. To analyze the performance of the proposed method, simulations for S-type trajectory are carried out. The results show that performance of EKF and UKF are the almost same when the initial heading error is smaller than $30^{circ}$, but UKF has a better performance for large initial heading error about $45^{circ}$.