Segregation in the blast furnace (BF) charging system is a significant challenge, as it can negatively affect the burden permeability and reduce BF efficiency. The discrete element method (DEM) is a valuable tool to gain insights into segregation dynamics in the BF. While previous DEM studies have extensively investigated segregation in the BF, the majority of them used the top hoppers as the starting point and assumed a pre-determined iron ore mixture composition (usually fully mixed state) within the top hopper. Considering the fact that the final segregation on the BF burden is significantly influenced by the degree of the segregation within the top hopper, it is crucial to precisely determine the degree of mixing of iron ore pellets and sinter within the hopper. In this study, we model the BF charging process from the stockhouse (i.e. weighing bunkers) until the top hopper at the industrial scale, aiming to elucidate how previous handling steps can affect the mixture composition within the hopper. Our findings reveal that the degree of mixing of pellets and sinter within the weighing bunkers (WBs) significantly influences the quality of mixing within the top hopper. Under the current practice where each materials are charged into separate WB, they are significantly segregated in the top hopper. We also demonstrated that mixing pellets and sinter before charging them into the WBs, can significantly reduce segregation within the hopper. The results of this study enhance our understanding of the segregation phenomenon in the BF charging system, providing insights that can be used for optimising the charging process.