Revealing the microdynamic mechanism and thermodynamic properties of the gelling process of waxy crude oil at the microscale plays an important role in ensuring the safe production and transport of waxy crude oil. However, few studies have dealt with the influence of paraffin molecular branching position on the gelling process. The focus of this study is to clarify the influence of branching distribution on molecular aggregation through molecular simulation, so as to further improve the mechanistic study of the gelling process of waxy crude oil. A variety of molecular models of crude oil systems containing paraffin molecules with different distributions of branched chains, asphaltenes, and light oils are developed to analyse the molecular aggregation and wax precipitation characteristics during the gelling process.The results show that the paraffin molecular chain morphology gradually from stretching to curling and the molecules gradually from dispersing to aggregating during the temperature drop process. From the van der Waals force analysis, it is concluded that isomeric alkanes with a close branching distribution form the weakest gelling structures. In addition, the phase transition temperature difference between n-alkanes and isoalkanes is large about 9 K, but the phase transition temperature difference between the two isoalkanes with different distributions of branched chains is small only about 3 K. This indicates that for alkanes with the same molecular formula, the length of the main carbon chain is a dominant factor in influencing the aggregation of the molecules and the gelling properties of the crude oil system. Under high temperature conditions, isomeric alkanes have the best mobility and are most sensitive to temperature. The results of the study can provide help for the mechanism of the gelling process of waxy crude oil to ensure the safety of the pipeline transmission process, and provide theoretical guidance for the production of depressants and catalysts.