To solve the problem of saltwater intrusion, the saltwater intrusion characteristics and salinity transport mechanism in the south branch of the Dongjiang River were analyzed based on three-dimensional numerical simulation. The results show that the change of saltwater intrusion in the Dongjiang River has the same periodicity as that of tidal level, and the maximum salinity occurs during the spring tide in a period of spring, moderate, and neap tides. The south branch of the Dongjiang River is generally in a state of full mixing to partial mixing of salinity, and the salinity distribution is uniform in the vertical direction. The occurrence of saltwater intrusion in the Dongjiang River depends on the contrast between the effects of runoff and tidal current, and there is almost no vertical circulation transport. Therefore, increasing the runoff discharge is the most effective measure to reduce the saltwater intrusion in the Dongjiang River.