We have developed and presented a comprehensive toolbox for in silico studies of Martini 3 LNPs, offering a robust platform for advancing nucleic acid delivery systems. This toolbox includes an extensive library of ionizable lipids and naturally occurring sterol models, specifically designed for Martini 3, which can serve as essential building blocks in the study of LNPs. Additionally, we provide a detailed protocol for constructing full-scale LNPs, guided by experimental data such as cargo contents, PEGylation, lipid formulation, hydration levels, internal ion concentration, and N/P ratio. Moreover, we have introduced a protocol for screening and quantifying the fusion efficacy of various LNP formulations. These models and protocols not only enable the detailed study of LNP organization, structure, and fusion but also pave the way for routine screening of lipid mixtures, prediction of LNP stability, and optimization of fusion efficacy. Through our showcase of Martini 3 LNP applications in fusion assays, we have demonstrated the critical role of endosomal negatively charged lipids in enhancing transfection efficiency and identified trends in fusion efficiency across different LNP compositions. This underscores the importance of accurately modeling the endosomal membrane to improve LNP predictions. Simulating whole LNPs with our toolkit can possibly provide, in the future, additional insights into how lipid formulation influences corona formation in the bloodstream, which is also a critical factor for LNP internalization into cells.