A fiber structure manufacturing apparatus that includes: a defibration unit that pulverizes and defibrates a raw sheet material that contains fibers; a transportation unit that transports a defibrated material after defibration by the defibration unit; a forming unit that forms a fiber structure from the defibrated material transported by the transportation unit; a temperature acquisition unit that acquires a temperature inside the defibration unit; and a control unit that controls a mass flow of gas that contains the defibrated material transported from the defibration unit in accordance with the temperature acquired by the temperature acquisition unit.