The works aims to propose a new versine square shaped curve acceleration and deceleration algorithm to improve the motion stability of stacker and solve the problem of sudden impact of the traditional S-shaped curve acceleration and deceleration algorithm which affects the instantaneous amplitude of stacker column due to the discontinuous jerk. By deducing the vibration equation of the stacker column structure, an acceleration and deceleration algorithm model with versine square function as the core was constructed. Also, the Simulink vibration simulation model was built. Then, it was substituted into the Simulink vibration model together with the traditional S-shaped and versine shaped curve acceleration and deceleration algorithms for comparison and simulation, and the column amplitude results were also analyzed. Compared with the traditional S-shaped curve acceleration and deceleration method, the column amplitudes of the versine and the versine square shaped curve acceleration and deceleration algorithms were reduced by about 2.6% and 4.2% respectively. The velocity, acceleration and jerk curves of the versine square shaped acceleration and deceleration algorithm are all continuous. The stability and the column amplitude of the stacker based on the new proposed algorithm are taken into account simultaneously. Compared with other algorithms, the control result is better.