Messenger RNA (mRNA) encapsulated in lipid nanoparticles (LNPs) represents a cutting-edge delivery technology that played a pivotal role during the COVID-19 pandemic and in advancing vaccine development. However, molecular structure of mRNA-LNPs at real size remains poorly understood, with conflicting results from various experimental studies. In this study, we aim to explore the assembly process and structural characteristics of mRNA-LNPs at realistic sizes using coarse-grained molecular dynamic simulations. The largest system, representing a real-sized LNPs (∼ 80 nm), reaches up to ∼6 million beads, around 30 million atoms. Moreover, the impacts of different mRNA loading levels and pH changes on the structure of mRNA-LNPs are also examined. Under acidic pH, ionizable lipid (dilinoleylmethyl-4-dimethylaminobutyrate, MC3), helper lipid (cholesterol, CHOL, distearoylphosphatidyl choline, DSPC), and mRNA rapidly self-assemble into spherical-like LNPs within 50 ns, with a diameter of 51.2 nm (2 mRNA) and 75.8 nm (4 mRNA). Inside the LNPs, a continuous lipid phase is observed alongside an aqueous phase, forming a bicontinuous structure. CHOL and DSPC form lipid rafts distributed within the shell or core layer of the LNPs, enhancing rigidity and stability. Notably, mRNA aggregation within the LNPs occurs independently of the lipid environment, and different mRNA payloads significantly influence the lipid composition between the core and shell. At neutral pH, lipid clustering slightly reduces the retention capacity of LNPs for mRNA. Our findings highlight the presence of a bicontinuous structure and lipid rafts in self-assembled LNPs, which critically influence LNPs rigidity, fluidity, and mRNA delivery efficiency. This structural insight provides a foundation for the rational design of LNPs to optimize mRNA delivery in future applications.