One suspect was arrested and a large quantity of bomb-making materials and weapons were seized in Pattani's Nong Chik district.
One man, who confessed to being a bombmaker, was arrested.
Bomb-making materials found inside included kerosene to mix with the chemical urea, a boat-load of gun powder, ball bearings, and two large gas cylinders, each weighing about 15 kilogrammes, a solar panel as well as a large number of firearms.
Another cottage used for sleeping and cooking had a shotgun with 20 rounds of ammunition and a large quantity of petrol inside.
The third cottage served as sleeping quarters, a meeting room and a prayer room.
Two bombs made using 15kg gas cylinders, copies of the Koran, clothes, hammocks and a large quantity of survival gear were found inside the building.
The base was believed to have been in use for at least two years.