Asphaltene can exist in both the dispersed state and the aggregated state in crude oil. Because of the changes in crude oil composition, pressure, or temperature, the asphaltene transition from dispersed asphaltene to aggregated asphaltene will occur and then influence the wax crystallization, gelation, and flow behavior of crude oil. In this paper, the asphaltene transition was realized by mixing two different crude oils for different times. The aggregated asphaltene was characterized by the optical microscopy and centrifugation-based separation method. The effects of asphaltene transition on wax crystallization, gelation, and flow behavior of crude oil were investigated by differential scanning calorimetry and rheological measurements. The results show that the aggregated asphaltene can serve as a crystal nucleus for wax molecules, promoting the wax precipitation, weakening the strength of the network of wax crystals, and delaying the gelation process of crude oil. On the other hand, the dispersed asphaltene can serve as the connecting point between wax crystals, accelerating the gelation of crude oil, and increasing the gel strength. The viscosity measurements below the wax appearance temperature show that the viscosity of crude oil increases because of the interaction between aggregated asphaltene and wax.