The particle diameter distribution of sinters ore in vertically arranged cooler leads to serious segregation, which will greatly reduce the heat recovery efficiency of vertically arranged cooler. In order to solve the segregation problem of sinters ore, the simulation of the original vertically arranged cooler form domestic steel plant was conducted, which was based on discrete element method with graphics processing unit parallel computing. In the feeding process, the behaviors of sinter ore and their distribution of diameters were studied. The simulation results showed that the difference of movements of particles, which was caused by diameters of different sinters ore, increased with the height of sinters ore dropping from the bunker. Furthermore, larger sinters ore would aggregate in the corners and small sinters ore would aggregate around the point of falling sinters ore, which was due to the lack of internal structures restricting their movements, leading to more serious of segregation happen. Thus, a hopper and the inclined fences were introduced in the top and around the bottom of the storage bin, respectively. The hopper, which turned original design to two-layer storage bin, aimed to reduce the height and tailor the direction of the sinter ore dropping from the bunker, and thus the difference of the velocities and moving behaviors for the sinters ore of different diameters would be reduced greatly. The inclined fence aimed to restrict the movements of the largest sinters ore, so that their aggregation would be reduced. The simulation results of the new structure, including the distribution of the average diameter, the evolution of the segregation and the standard deviation of the average diameter of sinters ore, indicated that the new structure was advantageous in solving the segregation problem of sinters ore in the vertically arranged cooler.