Two-dimensional (2D) materials have attracted intensive interest because of their unique optical and electronic properties, their potential applications in next generation electronic devices, as well as serving as an ideal platform to explore new physics or chemistry at the 2D limit. As an atomically thin layered material, their atomic/electronic structures and device performances are susceptible to the various surfaces presented. In this regard, plenty of surface modification approaches have been applied to enrich their functionalities and complement their limitations. In this review, we summarize the state-of-the-art progress on the surface engineering of graphene and transition metal dichalcogenides (TMDCs). We begin with the defect and single-atomic incorporation in graphene lattice and surface transfer doping of graphene, followed by the bandgap and mobility engineering, and the construction of versatile heterostructures of TMDCs. Although this review mainly focuses on graphene and TMDCs, it is not an exhaustive list of the experimental results, but it rather summarizes the established knowledge in surface engineering and pinpoints the most promising future trends. These surface engineering approaches can also be applied to other 2D materials, such as phosphorene and antimonene.