Deposition of wax on a cold surface is a serious problem in oil production. Progress in developing more effective wax inhibitors has been impeded by the lack of an established mechanism connecting the molecular structure to inhibitor efficiency. Some comb-like polymers having long alkyl side chains are known to decrease the rate of wax formation. Among several possible mechanisms, we investigate here the incorporation-perturbation mechanism. According to this mechanism, the inhibitor molecules in oil are preferentially partitioned (incorporation) toward the wax-rich (amorphous) wax deposits (soft wax), which then serves as a perturbation to slow down the ordering transition of soft amorphous wax into more stable but problematic hard wax crystals. Indeed, molecular dynamics simulations on an effective inhibitor molecule in both the oil phase and in the amorphous wax phase support the idea that the oil-to-wax partition of the inhibitor is energetically favorable. With the inhibitor molecule embedded, the structure of wax crystal is disturbed, significantly decreasing the order and significantly lowering the cohesive energy density relative to that of the pure wax crystal, supporting the slower transition from soft wax to hard wax. Thus, in the presence of an effective wax inhibitor, crystallization (formation of hard wax) is slowed dramatically, so that there is time to flush out the soft wax with a high-pressure flow inside the pipeline. This suggests design principles for developing improved wax inhibitors.