At high temperature, silicon oxycarbide (SiCO) exhibits excellent mechanical properties and thermal stability. The incorporation of boron in SiCO results in improved performance in creep temperatures. In this work, large-scale molecular dynamics calculations were applied to obtain amorphous SiCO structures containing boron. Phase separation of C-C, B-C and Si-O was achieved for three compositions, and silicon-centered mixed-bond tetrahedrons were reproduced successfully. As the boron content increases, the boron atoms tend to form B-C and B-Si bonds in the voids, which stretches the free carbon network in some instances, causing a increase in C-C distance. Young's modulus remains stable at high temperature for the high-carbon case, which indicates that the free carbon network plays a critical role in the structural and thermal stability of SiBCO. Graphical Abstract Three major typical structures in the cooling down process for silicon boron oxycarbide (SiBCO). Bonds: red Si-O, blue Si-C, black C-C, green B-C, purple Si-B.