Seven of the region's cities, including the capital Nanning, and 17 counties reported heavy rain, according to the regional civil affair bureau.
The deceased was killed when a building collapsed and the missing was swept away by a flood, the bureau confirmed, state-run Xinhua news agency reported.
Liuzhou City, one of the worst-hit areas, reported serious floods in its downtown area. Roads are impassable, cars are submerged, public transport has been suspended, and several trains were delayed.
The city railway department had to use boats to ferry train drivers to the station.
According to the National Meteorological Center, heavy rain will continue in the north part of the region tonight and tomorrow.