The aggregation behavior and the subsequent deposition behavior of wax crystals own undesirable effects on the production and transportation of waxy crude oil. The understanding and prediction of these behaviors are essential to ensure economic and uninterrupted flow of waxy crude oil when the oil temperature decreases below the wax appearance temperature (WAT). In this paper, a novel method of fractal dimensional analysis was introduced to elucidate the aggregation behavior of wax crystals in different shear flow fields. The fractal methodology for characterizing wax crystal aggregation was then developed, and a blanket algorithm was introduced to compute the fractal dimension of the aggregated wax crystals. Considering the flow characteristics of waxy crude oil in a pipeline can be correlated with the shearing stress work, a modified wax deposition model focusing on shearing energy analysis was established. The results indicate that a quantitative interpretation of the wax crystal aggregation behavior can be realized using the fractal methodology. The aggregation behavior of the wax crystals is closely related to the temperature and shearing experienced by the waxy crude oil. The aggregation behavior will be intensified with decreasing temperature and shearing effect, and a wider fractal dimension distribution appears at lower temperatures when the same shear rate range is used. Furthermore, the improved model provides a method for discussing the effects of the operating conditions on wax deposition. The average relative deviation between the improved model prediction results and experimental results from the literature is 3.01–5.32%.