In this article, the effect of semi-analytical alignment error on the performance of the navigation system has been investigated. Although investigating the effect of various error-causing factors on the performance of the navigation system is not a new issue, the conducted investigations show that the effect of the alignment error has not been studied in the semi-analytical working regime. To perform this analysis, after introducing the related coordinate frames, the ideal and real functional equations of the navigation system in the desired working regime were extracted and then the performance of the navigation system was analyzed by taking into account the errors of horizontalization and initial orientation. The results have been showed that although the presence of this error causes errors in the navigation parameters, this error does not increase with the passage of time and has Shuler and day and night periods. It was also shown that the initial orientation error of the stable platform does not play a role in the calculation error of horizontal velocities and longitude and latitude, and the bias that occurs in the error of determining the side angle of the stable platform is equal to the initial orientation error of the stable platform.