Organized assemblies formed by amphiphilic molecules have various structures, including micelles, microemulsions, vesicles, lamellar liquid crystals, and hydrogel. Due to the similarity between the basic structure of the life system and molecular organized assemblies, these organized assemblies are of much importance as a convenient model for studying the biomacromolecules such as protein and phospholipids bilayer and also of great significance from the viewpoint of various promising practical applications. Therefore, it is of great theoretical and practical significance to study the interaction between organized assemblies of amphiphilic molecules and biological active molecules. In recent years, we have carried out a series of work in this area. We designed and synthesized some amino acid, glucoside and ionic liquid based functional green surfactants. These new surfactants can self-assemble into organized assemblies having various structures, such as micelles, vesicles, lamellar liquid crystals, and hydrogel. The mutual transformation among these different molecular ordered assemblies can be regulated by the molecular structure of surfactants and environmental factors. The molecular self-assembly of surfactants based on noncovalent interactions, such as hydrogen-bond, static electricity, solvophobic interaction and π-π stacking, etc, provides a powerful tool for the creation of well-defined structures in certain dimensions, and the transform among these organized assemblies. Furthermore, the interaction relationship between amphiphilic molecules and biological active molecules has been revealed by studying their thermodynamic and kinetic characteristics. Methemoglobin and GDA/ n -C5H11OH/H2O assemblies can affect their structures and properties, and the change in behavior is dependent on the content of methemoglobin and the composition and structure of the GDA/ n -C5H11OH/H2O system. The existence of methemoglobin reduces the hexagonal liquid crystal region, while the lamellar liquid crystal region is little changed in the presence of methemoglobin. The addition of amino acid does not change the structure of the microemulsions ultimately, but results in the redistribution of surfactants between the upper and lower phases. Furthermore, the distribution of amino acid between the phases can be adjusted by changing the total surfactant content. The exact location of the drugs depends on both the micellar structure and the molecular structure. The different locations of drugs in the micelle influence the structure-function of the drugs. Flavonoids show selective dimerization with the micelle structure change. It is always in the form of a dimer in spherical micelles, while it is in the form of a monomer in the rodlike micelles. The antihydrolysis and antioxidation activity of drug molecules can be modulated by changing and adjusting the microstructure of the molecular ordered assemblies. The clearance of hydroxyl radicals by morin and the protection of human serum albumin against hydroxyl radical induced damage by morin have been reduced in the Triton X-100 micelles. This dynamic process of puerarin’s localization in micelles causes the acid–base equilibrium of puerarin to move to the deprotonation reaction, enhancing the interaction between puerarin and surfactants, and promoting the formation of the puerarin–surfactant associate. With the changes of membrane hydrophobicity the effect of puerarin on membrane-water interfaces enhances and puerarin can locate more internally in the region of membranes, favoring the deprotonation of puerarin. Based on this, the relationship between the structure-function of bioactive molecules and the microenvironment is clarified from molecular level. This provides important theory and application basis for life sciences, medicine, pharmacy and other related fields.