The invention discloses a freeze-dried fruit processing system. The freeze-dried fruit processing system comprises a vacuum freeze drying machine, a near-infrared spectral detector and a controller, wherein the near-infrared spectral detector is used for acquiring a near-infrared spectrum of a to-be-detected fruit in a vacuum freeze drying machine; the controller stores a control instruction and is used for controlling the vacuum freeze drying machine to work; and the controller also stores a water content quantitative analysis model of different freeze-dried phases of a standard fruit sample,the controller determines the water content of the to-be-detected fruit near-infrared spectrum according to the water content quantitative analysis model of different freeze-dried phases, the controller judges whether the water content of the to-be-detected fruit reaches the water content of the standard fruit sample of the current freeze-dried phase, and if yes, the controller controls the vacuum freeze drying machine to adjust the freeze-drying control data or to stop working. By adopting the near-infrared spectrometer to detect the water content of the fruit in the freeze-dried processingprocess, the freeze-dried control data is automatically adjusted according to a detection result, so that not only can the energy be saved, but also the quality of the freeze-dried fruit can be ensured.