The wellbore fluid flow characteristics and hydrate flow assurance problems during the deep-water gas well cleanup process seriously affect the safety of gas well testing. Aiming at the process of deep-water gas well cleanup where the liquid gas ratio changes dramatically, this study reveals the distribution law of gas−liquid flow patterns in the wellbore. Combined with the clean test conditions of deep-water gas wells, the transient numerical simulation and analysis are carried out. At the same time, a hydrate risk prediction model suitable for the well cleanup process is established to predict the hydrate risk under different cleaning conditions. The research results are as follows: (1) after flowback, the temperature at the wellhead and mud line presents different characteristics of temperature change, the wellhead temperature decreases first and then increases, while the flow temperature at the mud line rises first and then decreases; (2) slug flow and annular flow are more likely to occur in the wellbore under low wellhead pressure. Bubble flow often appears in the initial stage of flowback under high wellhead pressure and gradually changes into slug and annular flow patterns in the middle and late stages; (3) at the same flowback time, the wellbore will also present different flow patterns along the way. The lower part of the well bore mainly presents bubble flow and slug flow, and the upper and middle parts of the well bore mainly present annular flow patterns; (4) high liquid−gas ratio conditions, proper well cleaning speed, and the use of hydrate inhibitors can effectively reduce the hydrate risk during the cleaning process of deep-water gas wells.