Molecular dynamics was employed to investigate the micro-mechanism of water and asphalt on hydrate aggregation, addressing the mechanism of aggregation caused by hydrates, asphalt, and water droplets in pipelines. In low-water-content pipelines, the oxygen atoms in asphalt form hydrogen bonds with hydrates, anchoring them to the hydrates. Asphalt forms stable molecular films through π-π interactions, effectively preventing hydrate aggregation. In addition to traditional hydrogen bonds (bond energies around 18 kJ/mol), asphalt also form π hydrogen bonds (bond energies around 9 kJ/mol), making it easier to bind with water. The water droplets reduce the face-to-face stacking of asphalt molecules from 35.63 % to 30.63 %. Hydrogen bonds drive asphalt to approach water droplets, and the number of hydrogen bonds between asphalt and water droplets is almost 3 times that between asphalt and hydrates. This greatly disrupts the pre-existing asphalt films between hydrate particles and weakens the anti-aggregation effect. Water bridges between hydrate particles further promote hydrate aggregation. In the HWA model, hydrate particles begin to aggregate at 27.15 ns. Water droplets can easily change the distribution status of asphalt and other anti-agglomeration agents. When designing anti-agglomeration agents, it is necessary to consider maintaining the stability of water droplets to prevent water diffusion.