Lipid-based drug delivery systems are considered as promising vehicles for hydrophobic drug compounds. Lipid distribution within the droplet can affect drug loading capacity in these carriers. However, it is extremely challenging to determine the nanostructure within these carriers through the implementation of the direct experimental methods due to the ultrafine size. Therefore, coarse grained molecular dynamics (MD) simulation was utilized to model different kinds of lipid-based nanoparticles of the diameter about 12 nm including solid lipid nanoparticles (SLN), nanoemulsion (NE), and nanostructured lipid carriers (NLC), and the organization of the lipids within the carriers was explored. The aforementioned nanoparticles consisted of stearic acid, oleic acid as lipids, and sodium dodecyl sulfate (SDS) as a surfactant in water medium. Furthermore, the impact of solid to liquid mass ratio on the lipid distribution within the lipid matrix was investigated regarding the NLC simulations. In the equilibrium state, we observed the vesicle-like structure for all the investigated systems in which the hydrophilic moieties of the lipids and surfactant organized a semi-bilayer fold into the droplet and the hydrophobic tails accumulated among them. It is worth mentioning although SDS as a harsh surfactant, which is a special case, was expected to be present in the surface of the droplet, it penetrated into the lipids. Additionally, our results showed remarkable entrapped water beads inside the droplet in the form of one or more cavities along the internal layer of the head groups which was surrounded by lipid head groups. It was also reported that in the building structure of the nanoemulsion and SLN, in the central parts of the droplets, lipids were denser than the case of NLCs. Moreover, no crystallization occurred within the lipid-based carriers. Finally, the results indicated that, in the case of NLC simulations, the lipid distribution within the lipid matrix was insensitive to the mass fraction of solid to liquid lipids.