Molecular self-assembly (MSA) refers to spontaneous arrangement of molecular building blocks into ordered structures governed by weak interactions. Due to its high versatility and reversibility, MSA has been widely employed as a robust bottom-up approach to fabricating low-dimensional functional nanostructures, which are used in various applications in nanoscience and technology. To date, tremendous effort has been devoted to constructing various MSAs at surfaces, ranging from self-assembled monolayers and two-dimensional (2D) nanoporous networks to complex 2D quasicrystals and Sierpiński triangle fractals. However, precise control of the assembled structures and efficient achievement of their full applicability remain two major challenges in the MSA field. As another widely employed bottom-up approach to fabricating nanostructures, on-surface reaction (OSR) refers to a reaction that occurs on the surface and is two-dimensionally confined. OSR offers the possibility to synthesize compounds that may not be feasibly achieved in solution chemistry. Compared with MSA based on weak intermolecular interactions, OSR-based structures possess high thermal and chemical stabilities due to internal strong covalent bonds. In this Account, we briefly overview recent achievements of MSAs on single crystal metal surfaces with a focus on their controllability and applicability in tweaking the properties of the molecular building blocks involved. Emphasis will be particularly placed upon mediation of OSRs with the MSA strategy. To explore surface MSAs, on the one hand, scanning tunneling microscopy and spectroscopy have been routinely employed as the experimental tools to probe the intermolecular interactions as well as geometric and electronic structures of the assemblies at the atomic and molecular levels. On the other hand, density functional theory and molecular dynamics have been theoretically applied to model and calculate the assembling systems, furthering our understanding of the experimental results. In principle, MSA is primarily balanced by molecule-molecule and molecule-substrate interactions under vacuum conditions. In terms of the assembling methodologies, people have been attempting to achieve rational design, accurate prediction, and controllable construction of assembled molecular nanostructures, namely, tentative design of specific backbones and functional groups of the molecular building blocks, and careful control of the assembling parameters including substrate lattice, temperature, coverage, and external environment as well. An obvious goal for the development of these methodologies lies in the ultimate applications of these MSAs. MSA can retrospectively affect the properties of the assembling molecules. For instance, self-assembled structures not only can serve as secondary templates to host guest molecules but also can stabilize surface metal adatoms. In fact, the electronics, magnetism, and optics of MSAs have been successfully explored. In surface chemistry, the MSA strategy can be further applied to mediate OSRs in at least three aspects: tweaking reaction selectivity, changing reaction pathway, and restricting reaction site. The governing principle lies in that the self-assembled molecules are confined in the assemblies so that the pre-exponential factors and the energy barriers in the Arrhenius equation of the involved reactions could be substantially varied because the subtle reaction mechanisms may change upon assembling. In this sense, the MSA strategy can be efficiently exploited to tune the properties of the assembling molecules and mediate OSRs in surface chemistry.