The invention discloses a method for performing transfer alignment on a large azimuth misalignment angle of a ship in a polar region environment based on unscented Kalman filtering. The method comprises the following steps: I, completing starting and preheating preparation of a slave inertial navigation system, wherein the slave inertial navigation system completes primary binding by utilizing navigation parameters transmitted by a master inertial navigation system; II, performing inertial navigation calculation on the slave inertial navigation system, and synchronously acquiring the speed and attitude information of the master and slave inertial navigation systems output in a grid system to obtain speed and attitude errors so as to constitute and measure Z; III, according to navigation mechanics arrangement in the grid system, combining a grid navigation error equation, adopting a 'speed + attitude' matching manner, and establishing a system state equation and a measurement equation in the grid system; and IV, performing unscented Kalman filtering calculation, estimating the attitude misalignment angle of the slave inertial navigation system and the speed state estimated value, and completing transfer alignment. According to the method disclosed by the invention, the problem that the large azimuth misalignment angle cannot be subjected to transfer alignment in the polar region environment is solved, and the transfer alignment accuracy and applicability of the polar region are improved.