In high dynamic environment，accelerometer size effect becomes a dominant error effect source for accurate navigation of Strapdown Inertial Navigation System(SINS). In this paper, the mechanism of size effect error, which is due to separate acceleration measurement points, was analyzed theoretically as well as size effect error caused by RLG dither. The error model of the accelerometer size effect was derived. Considering the non-orthogonal installation scheme of the accelerometer triad, dynamic calibration model involving size effect compensation was derived. Using the navigation velocity as the observation, a general error equation for the accelerometer triad was established. Through a convenient test scheme, the parameters of the size effect were determined. A series of swaying tests showed that the size effect error compensation could effectively improve the navigation accuracy.