The invention relates to the technical field of flammulina velutipes industrialized cultivation equipment, in particular to a harvesting and waste recovery system of flammulina velutipes industrialized bottle cultivation. The system comprises a harvesting room, a recovery room and a culturing bottle group, a flammulina velutipes harvesting device is arranged in the harvesting room, the recovery room is internally provided with a waste recovery device, the flammulina velutipes harvesting device comprises a flammulina velutipes root conveying machine, a finished product flammulina velutipes conveying machine, a harvesting device rack, a cutter, a translation supporting frame, a first lead screw, a first lead screw driving motor, a clamping plate supporting frame, a clamping plate supportingframe lifting and lowering air cylinder, a second lead screw, a second lead screw driving motor and a clamping plate unit, the waste recovery device comprises a pneumatic cultivation bottle cleaning device and a waste conveying machine, the pneumatic cultivation bottom cleaning device comprises a recovery device rack, a cultivation bottle group turning device, an air spraying device and a cultivation bottle rotary driving device. By means of the system, harvesting efficiency can be improved, an air spraying pipe is prevented from damaging, and the cleaning effect is improved.