For the stable supply of oil and gas resources, industry is pushing for various attempts and technology development to produce not only existing land fields but also deep-sea, where production is difficult. The development of flow assurance technology is necessary because hydrate is aggregated in the pipeline and prevent stable production. This study established a system that enables hydrate diagnosis in the gas pipeline from a flow assurance perspective. Learning data were generated using an OLGA simulator, and temperature, pressure, and hydrate volume at each time step were generated. Stacked auto-encoder (SAE) was used as the AI model after analyzing training loss. Hyper-parameter matching and structure optimization were carried out using the greedy layer-wise technique. Through time-series forecast, we determined that AI diagnostic model enables depiction of the growth of hydrate volume. In addition, the average R-square for the maximum hydrate volume was 97%, and that for the formation location was calculated as 99%. This study confirmed that machine learning could be applied to the flow assurance area of gas pipelines and it can predict hydrate formation in real time.