The main objective of this paper is to elucidate the influence of drug-carrier compatibility and preparation method on the properties of Paclitaxel (PTX)-loaded lipid liquid crystalline nanoparticles (LLCNs). Here, glyceryl monooleate (GMO), glycerol monolinoleate (GML), glyceryl monolinolenate (GMLO) were selected as the lipids, and Soluplus, Poloxamer 407 (P407), Tween 80 were selected as the stabilizer to prepare LLCNs. First of all, PTX-carrier compatibility was screened by molecular dynamic simulation using Flory-Huggins interaction parameter as the criteria. Thereafter, PTX-loaded LLCNs were prepared under different energy input conditions and were characterized. Influence of lipid type, stabilizer type, drug-lipid ratio and preparation method on properties of the LLCNs was explored. It was found that both lipid and stabilizer type had significant influence on drug encapsulation efficiency. Compared to the LLCNs prepared under high energy condition, PTX-loaded LLCN prepared under low energy input had higher drug encapsulation efficiency, smaller particle size (211.6 nm versus 346.8 nm) and a sustained release behavior. In conclusion, molecular dynamic simulation is an effective tool to select the most appropriate composition of LLCNs for a specific drug substance, and LLCNs prepared using low energy input methods was particularly applicable for industrial manufacture. Copyright © 2021 American Pharmacists Association. Published by Elsevier Inc. All rights reserved.