This paper reports the adsorptions behavior of the 9,9'-Dixanthylidene on Ru(0001), the bottom-up fabrication of graphene was also investigated through a Scanning Tunneling Microscope (STM). We analyzed the spatial structure of 9,9'-Dixanthylidene molecules which were randomly dispersed on the Ru(0001) substrate in the sub-monolayer coverage. Then we bottom-up fabricated the graphene on 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°) were found after high temperature annealing in an ultrahigh vacuum. This experiment 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).