Engineering the boundary structures in 2D materials provides an unprecedented opportunity to program the physical properties of the materials with extensive tunability and realize innovative devices with advanced functionalities. However, structural engineering technology is still in its infancy, and creating artificial boundary structures with high reproducibility remains difficult. In this review, various emergent properties of 2D materials with different grain boundaries, and the current techniques to control the structures, are introduced. The remaining challenges for scalable and reproducible structure control and the outlook on the future directions of the related techniques are also discussed.