The invention discloses an inertial navigation system alignment accuracy evaluation method. The method comprises the following steps: with differential GPS speed as external reference base, constructing an inertial navigation system alignment accuracy evaluation observation quantity, and performing extended Kalman filter calculation in combination with an inertial navigation system alignment accuracy evaluation nonlinear model; after each extended Kalman filter calculation cycle, inserting the calculation of an extended fixed-interval smoothing gain matrix, and storing the filter data in real time until the filter calculation is over; and performing reverse extended fixed-interval smoothing calculation by use of the stored filter data, and estimating the attitude misalignment angle at the moment when the inertial navigation system alignment is over to realize evaluation of the inertial navigation system alignment accuracy. The method can realize inertial navigation system alignment accuracy evaluation in the conditions of large azimuth misalignment angle and small misalignment angle, and has the advantages of strong robustness, small data storage capacity and high calculation efficiency.