Revealing the nature of chain packing in conjugated polymer nanoparticles (CPNs) is one of the important issues to polymer physics research. Surfactant-stabilized CPNs in water show significantly enhanced luminescence intensity in comparison to small molecular organic dyes and single polymer chains dissolved in solvents. The importance of the conjugated polymer structure in nanomaterials is undoubted. However, details of the relationship between alignment of conjugated polymer backbone in CPNs and its luminescent property have not been established. Furthermore, there are yet no methods that can predict the atom-resolved structure of conjugated polymer in the CPNs. Herein, we employ coarse-grained (CG) molecular dynamic simulations to investigate the structure of phase-separated film and the film shattering process for a mixture of poly[2,6-(4,4-bis(2-ethylhexyl)-4H-cydopenta[2,1-b;3,4-b'-dithiophene)-alt-4,7-(2,1,3-benzothiadiazole)] (PCPDTBT) and 1,2-dioctanoyl-sn-glycero-3-phosphocholine (D8PC). The pi-pi stacked structure of PCPDTBT is significantly enhanced when the ratio-of D8PC increases in both dried and water exposed film. We also show that the amount of D8PC is at least 2.5 times larger than that of PCPDTBT to wrap the conjugated polymer chain, and the direct retrieval of atomistic details is achieved through back-mapping from the morphology of CG. Finally, we confirmed that conjugated backbones inside the nanoparticles were completely shielded from the aqueous solution by the dense layers of alkyl chains, resulting in remarkably enhanced chain packing. These simulated results are correlated with experimentally observed structure through UV-vis-near-infrared (UV-vis-NIR) spectrometry, scanning electron microscopy (SEM), particle size analyzer (PSA), transmission electron microscopy (TEM), and grazing-incidence X-ray diffraction (GIRD).