Paraffin wax deposition has long been a vexing problem in industry. Especially, in offshore oil production, paraffin wax deposits and clogs pipes and containers because of low temperature, causing severe economic loss. It has been known that the crystallization of n-alkanes mainly causes the deposition of paraffin wax, which is necessary to understand the mechanism of the crystallization behavior of paraffin wax. We solve the challenge of describing the crystallization behavior of the alkane mixture system and evaluate the contributions of every carbon atom to crystallization based on the occupied volume, structure entropy, and order parameter. These results demonstrate that the middle atoms are the main contributor to crystallization, and the end atoms of n-alkanes are unfavorable for the crystallization of n-alkanes, showing that increasing the number of end atoms, for example, adding branched alkanes, will hinder the crystallization of paraffin wax. Furthermore, perhydrosqualene is chosen to study the inhibition of crystallization by adding branched alkanes. As there are different properties between the end and the middle atoms, based on the principle of dissolution with similar properties, a small number of branched alkanes will promote crystallization. Also, an inhibitory effect of the end atoms is observed when the proportion of branched alkanes increases to a certain percentage. Our simulation work describes the crystallization behavior of paraffin wax in detail, providing theoretical assistance for preventing and controlling paraffin deposition.