In order to elucidate a link between density and structure of liquid Si-M (M=Fe, Ni, and Ge) alloys, synchrotron x-ray diffraction experiments have been conducted with the use of a conical nozzle levitation technique. Liquid structure factors of the Si-Fe and the Si-Ni alloys indicate a correlation of medium range ordering with the increase of the Si content. Although the total molar volume expands with the increase of the Si content in these alloys, the concentration dependence of the average interatomic distance shows a minimum around 70 at.% Si content. On the other hand, the Si-Ge alloys shows tendency of concentration dependence as ideal mixture in both total molar volume and the average interatomic distance. These results were discussed taking into account the formation of anisotropic bonds between 3d transition metal and Si atoms, which may induce a spatial expansion in the microscopic scale.