Highly efficient removal of impurity Bi element from scrap brass can facilitate the recycling process of brass. The effects of melting temperature, holding time and Mg-Ca alloy content on the removal effect of impurity Bi element were investigated by compound-separation method. The mechanism of the compound-separation method was revealed for removing the Bi element from a thermodynamic point of view. The results showed that the Bi content was decreased from 1.95 wt.% to 0.178 wt.% at the optimum process parameters of melting temperature of 980 °C, holding time of 20 min, and Mg-Ca alloy content of 6 wt.%, achieving a removal rate of 90.9%. A small amount of Ca-Bi compound remained in the brass matrix after refining. NaF flux can effectively wet and adsorb Ca-Bi compounds due to its low viscosity and the function of lowering the surface tension, which facilitate the agglomeration and flotation of Ca-Bi compounds to the melt surface, thereby ensuring the sufficient removal of Bi element.