Natural gas + water-in-diesel emulsion + AA systems with and without wax were used to investigate the influence of wax crystals and their heat-and mass-transfer effect on hydrate formation from macroscopic and microscopic aspect in a flow system. Hydrate nucleation and initial growth were found to be a partially occurred phenomenon. Wax was found to prolong the hydrate induction time through two significant effects: one was the macroscopic heat-transfer effect produced by wax deposition with insulating effect, and the other was the microscopic mass-transfer resistance originating from the wax crystals that were adsorbed at or adjacent to the oilwater interface. Hydrate induction time shortened and became less scattered with the increasing initial pressure. Based on the heat-transfer theory of a flow system and the hydrate nucleation theory, an improved model for hydrate induction time prediction was developed by coupling calculation of hydraulics and heat-transfer and by introducing mass-transfer effect of adsorption of wax crystals. The findings of this work are meaningful for providing essential information and supports for the ongoing deep-sea oil and gas production and the application of hydrate-management strategies in the presence of wax crystals in a flow system.