Abstract: Disclosed is a method for joint estimation of stellar atmospheric refraction and star tracker attitude, including: capturing, by a star tracker, an image of stars, and recognizing the image to obtain a matching relationship between an observed star and a reference star; transforming the reference star to a terrestrial reference frame based on time and position of observation to obtain a true zenith distance of the reference star; calculating an estimated stellar atmospheric refraction based on a simplified atmospheric refraction model, the true zenith distance, and an initial atmospheric refractive coefficient, and subjecting the reference star to stellar atmospheric refraction compensation; calculating the star tracker attitude, and re-projecting the observed star to the terrestrial reference frame to calculate the observed stellar atmospheric refraction and the stellar atmospheric refraction error; if the observed stellar atmospheric refraction is misaligned with the estimated stellar atmospheric refraction