Under the background of carrying out the “potato staple food” strategy in China, it is of great significance to do more related researches of the potato crop. In this paper, the comparison and analyses of spectral differences of different potato cultivars in different periods were aimed to provide theoretical and technical support to the identification of potato varieties, the distinction of potatoes and other crops, the extraction of potato spatial distribution, the monitoring of potato pests and diseases, the impacts of potato stresses as well as the various crop identification studies and provide a new idea for the crop hyperspectral correlation research. What’s more, the canopy hyperspectral reflectance data of the early maturing potato cultivar (Favorite), the middle-late maturing cultivar (Yanshu 4) at the tuber stage and expansion stage were obtained through field experiments in Jilin area. Firstly, the noise was removed by the method of Savitzky-Golay filtering. Then the spectra of continuum removal were obtained by the method of continuum removal and 6 parameters (the maximum absorption depth, total area, left area, right area, symmetry and area normalized maximal absorption depth) were extracted. Meanwhile, the first-order derivatives were calculated using the filtered spectral reflectance data and the spectral reflectance data of continuum removal. On the basis of the comparison of the two spectral reflectance curves of different potato cultivars, 8 different indices of 3 groups (reflectance difference index, first order derivative difference index, spectral parameters of continuum removal difference index) were constructed as evaluation indices. The reflectance difference index and first order derivative difference index were calculated using the bands of green light at 550 nm, red light at 670 nm and near-infrared light at 760 nm. Furthermore, we quantitatively analyzed the hyperspectral differences of different potato cultivars using these difference indices. In this paper, the method of continuum removal was applied to the analyses of hyperspectral differences of different potato cultivars with different growth stages. The difference indices in the article finally achieved good evaluation performence. The results showed that: (1) Compared with the reflectance difference index and maximum absorption depth difference index, the first order derivative difference index, total area difference index, left area difference index, right area difference index, symmetry difference index and normalized difference index could show the hyperspectral difference of different potato cultivars well. The spectra of continuum removal partially magnified the hyperspectral differences of two different potato cultivars. (2) The wavelength position and growth period of the filtered spectra and the spectra of continuum removal with the largest difference were the same located at the wavelength of 671.24 nm on August 16. The value of maximum absorption depth difference index was only 0.01. The value of first order derivative difference index of the filtered spectra reached 0.977 at the wavelength of 673.55 nm on June 24. The value of the first order derivative difference index of the continuum removed spectra reached 47.87 at the wavelength of 759.74 nm on June 24, which worked the best in spectral difference analyses of different potato cultivars. Besides, the total area difference index, right area difference index, symmetry difference index and normalized difference index all reached the maximum on June 24, with the values of 0.13, 0.214, 0.205 and 0.113, respectively. The left area difference index value reached the maximum of 0.199 on July 24. (3) According to the quantitative evaluation results of the difference indices, we could see that the period with the biggest hyperspectral difference of the two different potato cultivars is in the medium-late stage of tuber stage of early-maturing variety and initial stage of tuber stage of medium-late maturing variety.