Atomically thin 2D materials exhibit strong intralayer covalent bonding and weak interlayer van der Waals interactions, offering unique high in-plane strength and out-of-plane flexibility. While atom-thick nature of 2D materials may cause uncontrolled intrinsic/extrinsic deformation in multiple length scales, it also provides new opportunities for exploring coupling between heterogeneous deformations and emerging functionalities in controllable and scalable ways for electronic, optical, and optoelectronic applications. In this review, we discuss (i) the mechanical characteristics of 2D materials, (ii) uncontrolled inherent deformation and extrinsic heterogeneity present in 2D materials, (iii) experimental strategies for controlled heterogeneous deformation of 2D materials, (iv) 3D structure-induced novel functionalities via crumple/wrinkle structure or kirigami structures, and (v) heterogeneous strain-induced emerging functionalities in exciton and phase engineering. Overall, heterogeneous deformation offers unique advantages for 2D materials research by enabling spatial tunability of 2D materials' interactions with photons, electrons, and molecules in a programmable and controlled manner.