Application-oriented patterned growth of transition metal dichalcogenides (TMDCs) and their heterojunctions is of critical importance for sophisticated, customized two-dimensional (2D) electronic and optoelectronic devices; however, it is still difficult to fabricate these patterns in a simple, clean, and high controllability manner without using optical lithography. Here, we report the direct synthesis of patterned MoS₂ and graphene–MoS₂ heterojunctions via selective plasma treatment of a SiO₂/Si substrate and chemical vapor deposition of MoS₂. This method has multiple merits, such as simple steps, a short operating time, easily isolated MoS₂ layers with clean surfaces and controllable locations, shapes, sizes and thicknesses, which enable their integration into the device structure without using a photoresist. In addition, we demonstrate the direct growth of patterned graphene–MoS₂ heterojunctions for the fabrication of transistor. This study reveals a novel method to fabricate and use patterned MoS₂ and graphene–MoS₂ heterojunctions, which could be generalized to the rational design of other 2D materials, heterojunctions and devices in the future.