Although the problem of wax deposition in multiphase transportation pipelines have been addressed and some related 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 behavior and developed a model for describing wax deposition path in oil/water two-phase flows. The impact of the emulsified water droplets on wax crystals aggregation in shearing flows was quantified using 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 pipeline wall was discussed by solving the developed model which involves the possible inclination angle of multiphase transportation pipeline. The availability of the mechanistic model was validated by the data and knowledge in the existing literature. The results indicated that wax crystals morphologies and structures tended to be regular with the enhancement of shearing effect, and their aggregation behavior were restrained. The circular degree and particle size of wax crystals showed a characteristic that it firstly 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 velocity for wax crystals depositing to pipeline wall decreased and the time for wax crystals depositing to pipeline wall extended with the existence of emulsified water droplets. The wax deposition path became more complex in multiphase transportation, and such effect became remarkable when the dispersity of oil/water two-phase enhanced. Accordingly, the intractable wax deposition of waxy crude oil in cold environment transportation would be mitigated to some extent. This study contributes to comprehending the distinction of wax deposition mechanism in single-phase and multiphase transportation of waxy crude oil, and the proposed method and model are valuable for further predicting wax deposition in waxy crude oil emulsions pipelines. The findings in this study also point out an approach to conducting cost-effective flow assurance operations in crude oil production and transportation.