The self-assembly of polymer grafted nanoparticles is more and more used in the field of functional materials. However, there is still a lack of analysis on the dynamic transformation paths of different self-assembly morphologies, which makes it impossible to achieve further precise regulation and targeted design in experiments and industrial production. In this work the effects of patchy property, grafted chain length, ratio and grafting density on the self-assembly behavior and structure of polymer grafted flexible patchy nanoparticles are investigated by dissipative particle dynamics simulation method through the construction of coarse-grained model of polymer grafted ternary nanoparticles. The influence and regulation mechanisms of these factors on the self-assembly structure transformation of flexible patchy nanoparticles are systematically studied, and a variety of structures such as dendritic structure, columnar structure, and bilayer membrane are obtained. The self-assembly structure of flexible patchy nanoparticles obtained in this work (such as bilayer membrane structure) provides a potential application basis for designing drug carriers. By precisely regulating the specific structural characteristics of the system, it is possible to achieve efficient loading of drugs and targeted delivery functions, thus significantly improving the bioavailability and effect of drugs.