It is essential to understand the structural properties of Fe-SiO2 melt for converting SiO2 inclusions into the reinforcing particles in Fe matrix by liquid metallurgical synthesis. In this work, the structural behaviors of Si and O in Fe27SiO2, Fe24(SiO2)2, Fe21(SiO2)3, and Fe18(SiO2)4 melts at 2800 K and the formation of SiOn clusters in Fe24(SiO2)2 melt (20 at.% SiO2) from 2800 K to 2000 K are investigated by ab-initio molecular dynamics simulations. According to the pseudo-binary mixing enthalpies, partial pair correlation functions, and chemical short-range order, the critical composition range for the formation of SiOn clusters in Fe-SiO2 melt at 2800 K is from 20 at.% SiO2 to 30 at.% SiO2, and the critical temperature range in the quenching process of Fe24(SiO2)2 melt is from 2600 K to 2400 K. By further analyzing the distribution of partial coordination numbers and bond angles, the quenching process of Fe24(SiO2)2 melt from 2800 K to 2000 K can be divided into three stages: the homogenous Fe-SiO2 melt from 2800 K to 2600 K, the dispersive formation of SiOn clusters containing a considerable number of SiO4 tetrahedrons from 2600 K to 2200 K, the gathering of SiOn clusters contributed by the connection of SiO4 tetrahedrons in the pattern of OSi2 from 2200 K to 2000 K.