The invention provides a flue-cured tobacco flue-curing barn control system and a control method thereof, and relates to the technical field of flue-curing of flue-cured tobacco. The flue-cured tobacco flue-curing barn control system comprises a flue-curing chamber (1), a heat pump unit chamber (2), a retaining wall (3), and a moisture exhaust passage (4). The moisture exhaust passage (4) is disposed below the flue-curing chamber (1). The flue-curing chamber (1) is adjacent to the heat pump unit chamber (2). The retaining wall (3) is horizontally arranged. The flue-curing barn is convenient toset up and install, has a long service life, and can greatly improve the utilization rate of heat energy by the use of the heat pump unit chamber, thereby reducing the labor cost. The control methodof the flue-cured tobacco flue-curing barn control system accurately controls the temperature and humidity of the flue-curing barn by controlling the return air, and guarantees the quality of the flue-cured tobacco strictly according to the requirements of the three-stage flue-curing process.