Speed of transfer alignment affects the ability of rapid response of the weapons equipped on the ship or the plane, so rapid transfer alignment has been widely researched for the last two decades. The “velocity plus attitude” matching rapid transfer alignment algorithm which is presented by the American scientist Kain, who started the times of rapid transfer alignment, then lots of researches have been done based on Kain’s work, every one has its own advantages, and of course disadvantages. Three rapid transfer alignment algorithms called “velocity plus attitude”, “velocity plus rate” and “attitude plus rate” matching rapid transfer alignment, have been compared from the aspect of accuracy and speed in this paper, while the flexure of the vehicle and the lever arm errors occurred respectively. Simulations have been done for the comparison of these three rapid transfer alignment algorithms, results show that while there is no flexure nor lever arm error, the three methods perform the same in accuracy and speed, the “velocity plus attitude” is a little slower than the other two methods in the estimation of the misalignment, the flexure influence the “velocity plus rate” and “attitude plus rate” matching methods much more than the “velocity plus attitude” method, but the latter greatly affected by the lever arm error. The results of this paper can help engineers to chose better rapid transfer alignment algorithm in their work.