A frequency selection method of NIR spectroscopy was proposed in the present paper for discrimination of maize seed varieties. A criterion function was defined to evaluate the discriminative ability of NIR spectroscopy at different frequencies, and then features of maize seed varieties were extracted accordingly for further processing. By eliminating correlation between features at different frequencies, the selected features are guaranteed to contain as much information of inter-variety difference as possible. Also, features with larger variances are preferred to suppress the impact of noise. Experiment results demonstrate that our frequency selection method can achieve high recognition rate with less spectroscopy features than traditional methods. Specifically, a recognition rate as high as 94.16% can be attained with NIR spectroscopy with only 30 frequencies. Simulation results show that recognition rate of NIR spectroscopy at selected frequencies is stable with small disturbance of frequencies, which verifies the robustness of the authors’ method.