Nematic liquid crystal materials designed for optics, microwave communication tuning, etc. need high response speed, which is related to the rotational viscosity and the birefringent index of the liquid crystal. In order to achieve a wide tuning range of phase modulation, the nematic liquid crystals often employ large π-electron conjugated systems and large polar groups to enhance the birefringence and dielectric anisotropy of the liquid crystal molecule, which, however, increases the viscosity of the liquid crystal material, deteriorating the response speed of the microwave device. Herein, we explore the viscosity of the nematic liquid crystal from the perspective of liquid crystal compound structure by testing the viscosity of our designed and synthesized forty-two different nematic liquid crystals by using a rotating rheometer at 25 ℃. To the best of our knowledge, the BPNN-QSAR quantitative structure-activity model between nematic liquid crystal molecular structure and viscosity is established for the first time. The correlation coefficient between the predicted value and the experimental value is <i>q</i><sup>2</sup> = 0.607 > 0.5, indicating that the model can be used to predict the viscosity performances of liquid crystal compounds. Besides, the molecular structure descriptors affecting the viscosity properties are explored. Based on the practical application and this model, seven liquid crystal molecules of two series with large birefringent index are designed and tested. The viscosity predicted by the BPNN model is smaller than that of the molecules of the same type and matches with the measured viscosity.