Connecting molecular building blocks by covalent bonds to form extended crystalline structures has caused a sharp upsurge in the field of porous materials, especially covalent organic frameworks (COFs), thereby translating the accuracy, precision, and versatility of covalent chemistry from discrete molecules to two-dimensional and three-dimensional crystalline structures. COFs are crystalline porous frameworks prepared by a bottom-up approach from predesigned symmetric units with well-defined structural properties such as a high surface area, distinct pores, cavities, channels, thermal and chemical stability, structural flexibility and functional design. Due to the tedious and sometimes impossible introduction of certain functionalities into COFs via de novo synthesis, pore surface engineering through judicious functionalization with a range of substituents under ambient or harsh conditions using the principle of coordination chemistry, chemical conversion, and building block exchange is of profound importance. In this review, we aim to summarize dynamic covalent chemistry and framework linkage in the context of design features, different methods and perspectives of pore surface engineering along with their versatile roles in a plethora of applications such as biomedical, gas storage and separation, catalysis, sensing, energy storage and environmental remediation.