This paper reports the adsorption behavior of the 9,9′-Dixanthylidene on Ru(0001), the bottom-up fabrication of graphene is also investigated through a scanning tunneling microscope (STM). We analyze the spatial structure of 9,9′-Dixanthylidene molecules which are randomly dispersed on a Ru(0001) substrate in the sub-monolayer coverage. Then we bottom-up fabricate the graphene on the Ru(0001) substrate with the 9,9′-Dixanthylidene molecules as the precursor. Three kinds of moiré superstructures with different rotation angles (6.3°, 13.9°, and 16.1°) are found after implementing high temperature annealing in ultrahigh vacuum. This result provides data support for the study of moiré superstructures on Ru(0001) substrate and lays a solid foundation for further scientific research based on graphene/Ru(0001).