Although the problems of wax deposition in multiphase transportation pipelines have been addressed and wax deposition models have been developed in recent years, the complex wax deposition paths derived from the potential variety of flow regimes in multiphase flow have not been well understood. This study presented a method for characterizing wax crystals aggregation and developed a model for describing the wax deposition path in oil−water two-phase flows. The effect of the emulsified water droplets on wax crystals aggregation in shearing flows was identified using the polarized light microscopy and image analysis method. The role of the emulsified water droplets in the wax deposition path reaching the upper side and lower side of the pipeline wall was discussed by solving the developed model which involves the possible inclination angle of the multiphase transportation pipeline. The availability of the mechanistic model was validated by the data and knowledge in the existing literature. The results indicated that the circular degree and particle size of wax crystals showed a characteristic that it first increased and then decreased with the accumulation of emulsified water droplets in shearing flow, and this transition appeared to the phase inversion point of the oil−water two-phase. The wax deposition path was complex in multiphase transportation. The velocity for wax crystals depositing to the pipeline wall decreased, and the time for wax crystals depositing to the pipeline wall extended with the existence of emulsified water droplets. This behavior became remarkable when the dispersion stability of the oil−water two-phase enhanced.