The tuning of flexible microscale friction is desirable for the reliability of wearable electronic devices, tactile sensors, and flexible gears. Here, the tuning of friction of atomically thin graphene on a flexible polydimethylsiloxane (PDMS) substrate was obtained with the elastic modulus using a 1H,1H,2H,2H-perfluorodecyltrichlorosilane (FDTS) self-assembly monolayers (SAMs)-modified microsphere probe with the diameter of 5 μm at the microscale. The friction can be tuned at a large scale with the difference in the elastic modulus of PDMS and thickness of graphene. The hydrophobic property of the FDTS SAMs-modified probe decreased friction by reducing interfacial adhesion and preventing the effect of capillary interaction; thus, the friction decreased with the increase in the elastic modulus of the PDMS substrate due to decreasing indentation depth and thus the interfacial contact area; and also, the enhanced out-of-plane stiffness effectively decreased the interfacial contact quality with the increase of the thickness of graphene. The flexible tuning of friction on graphene was further verified by the theoretical calculation from the aspects of the friction arising from the normal and lateral deformation around the contacting area. This work is meaningful for promoting the design and reliability of flexible micro-devices.