The invention discloses a near-infrared spectrum based method and a near-infrared spectrum based system for measuring the germination rate of a cotton seed, wherein the method comprises the following steps of obtaining a to-be-measured cotton seeds; carrying out near-infrared spectral scanning on the to-be-measured cotton seeds, so as to obtain the near-infrared spectral data of the to-be-measured cotton seeds; measuring the germination rate on of the to-be-measured cotton seeds according to the near-infrared spectral data of the to-be-measured cotton seeds and a cotton-seed germination rate measurement model, wherein the cotton-seed germination rate measurement model is previously established. The system is used for executing the method. The near-infrared spectrum based method and the near-infrared spectrum based system for measuring the germination rate of the cotton seed, which are provided by the invention, can be used for carrying out the near-infrared spectral scanning on the to-be-measured cotton seeds, obtaining the near-infrared spectral data of the to-be-measured cotton seeds and measuring the germination rate of the to-be-measured cotton seeds according to the near-infrared spectral data and the previously established cotton-seed germination rate measurement model; the measurement efficiency of the germination rate of the cotton seeds is improved.