The invention discloses an air-conditioning control system of killing crop pests by a biological floating bed, which belongs to the air-conditioning device for preventing plant diseases and insect pests and aims at providing an air-conditioning device for killing plant diseases and insect pests of water crops. The air-conditioning device comprises a biological floating bed, an air supply device and a tail gas recovering device, wherein a transparent plastic tent (1) is closely covered on the biological floating bed (2), the air supply device comprises a gas mixing box (5), an oxygen supply device (7) and a carbon dioxide supply device (8) and a nitrogen supply device (9) which are respectively and sequentially communicated with the gas mixing box through a reducing valve (14) and a flow meter (13), an air inlet pipe (3) communicated with the gas mixing box (5), and an air outlet pipe (12) communicated with the tail gas recovering device (10), and the air inlet pipe and the air outlet pipe are respectively led into the plastic tents (1). The invention has the advantages of no pollution and residue, safety, environment protection, good pest killing effect and the like, and is an ideal device for killing the plant diseases and insect pests of the water crops.