Abstract Rotation of nano-components is necessary in nanoscale mechanical systems (NMS) to enable various functions of nanomachines, however, the actuation and modulation of nanoscale rotation have been poorly investigated up to now. In this paper, we conduct molecular dynamics simulations to study the in-plane rotation of a graphene nanoflake hinged to a graphene substrate by easily accessible nanoindentation techniques. The flake can be driven to rotate by strain gradient fields (SGFs) induced by indenting the substrate locally. The effect of flake size, indenting velocity and position on flake rotation are studied systematically. It is found that there exists a critical range of flake size which is comparable to that of SGFs. The direction of flake rotation, i.e. clockwise or counterclockwise, can be tuned effectively by indenting the substrate asymmetrically with respect to the flake. Besides, the rotation can be speeded up by simply indenting more quickly. Furthermore, the flake can be trapped in a desired region on the substrate by adopting double SGFs. The continuous rotation of the flake can be realized by intermittently indenting the substrate near the flake. These results may be useful for designing the rotation of components in NMSs and nanoscale manipulation.