Sample stacking in capillary electrophoresis can concentrate sample species through the electrical field strength gradient caused by the inhomogeneous buffer concentration field in the capillary. The factors that affect the sample stacking process have been analyzed in detail by using the 1-D mathematic model developed in the previous paper. It has been found from the simulation results that the electrical charge number and the electrical charge sign of sample particles affect the electrophoretic velocity, which in turn has an important influence on the stacking process. The electrical potential can affect the migration time of sample particles to reach the detection window, and the initial length of the sample plug has significant influence on the maximal sample concentration after stacking and on the time to get the optimal stacking effect. The results obtained are helpful to the improvement of the sample stacking technique.