Biomolecular self-assembly plays a significant role for physiological function. Inspired by this, the construction of functional structures and architectures by biomolecular self-assembly has attracted tremendous attentions. Peptides can be assembled into diverse nanostructures, exhibiting important potential for biomedical and green-life technology applications. How to achieve the structural precise regulation of various nanostructures and functionalization by precise control of structures is the two key challenges in the field of peptide self-assembly. As the assembly process is a spontaneous thermodynamic and kinetic driven process, and is determined by the cooperation of various intermolecular non-covalent interactions, including hydrogen-bonding, electrostatic, p-p stacking, hydrophobic, and van der Waals interactions, the reasonable regulation of these non-covalent interactions is a critical pathway to achieve the two goals. To modulate these non-covalent interactions, one of the common used methods is to change the kinetic factors/external environment, including pH, ionic strength, and temperature, etc. These kinetic factors can effectively influence the interactions between peptides and solvents, resulting in dynamic and responsive variations in structures through multiple length scales and ultimate morphologies. However, the fatal disadvantage is the lacking of the precise regulation of assembled structures in the molecular level with consideration of both thermodynamics and kinetics. Compared with changing the external environment, the specific and precise molecular design is more favorable to achieve the structural precise regulation. The molecular structures and the component of building blocks can be rationally designed. For example, one can modulate the interactions between two or more than two building blocks by changing the physicochemical properties of each building block, enabling self-assembly and structural diversity of the final nanostructures. Furthermore, by combining peptides and other functional biomolecules (such as porphyrins), the functionalization of assembled nanostructures and architectures can be achieved more easily and flexibly. In this review, we will focus on the structural precise regulation and the functionalization of assembled peptide nanostructures. It is believed that the precise regulation of nanostructures is promising to promote the development of peptide-based materials towards green-life technology applications.