For samples with distinguishable echoes in detected transmission pulses, we mainly use the phase difference between the detected pulses to extract their refraction indices by transmission terahertz time-domain spectroscopy. Specifically, there are two methods. The first one requires the reference pulse and the first terahertz pulse transmitted through the sample; the second one requires the terahertz pulse transmitted through the sample and the second transmitted pulse after two reflections in the sample. However, in practice, there exists an angle between the incident terahertz beam and the surface normal of the sample. Yet, this angle is not easy to measure. So, in calculation we usually ignore this angle, which often causes error in the extracted refractive indices. In addition, this error is related with the selected method. In this article, after analyzing deviations of the refractive indices resulting from the angle when using the two methods, we propose a method to correct the extracting refractive indices. Our method could theoretically eliminate errors that are caused by the angle. Experiments further prove that this correction method is effective.