The development of an efficient method to patterning 2D MoS2 into a desired topographic structure is of particular importance to bridge the way towards the ultimate device. Herein, we demonstrate a patterning strategy by combining the electron beam lithography with the surface covalent functionalization. This strategy allows us to generate delicate MoS2 ribbon patterns with a minimum feature size of 2 μm in a high throughput rate. The patterned monolayer MoS2 domain consists of a spatially well-defined heterophase homojunction and alternately distributed surface characteristics, which holds great interest for further exploration of MoS2 based devices.