The assembly misalignment of a high maneuver precision guidance missile such as anti-air interceptor could have poor influence on the performance of the system and lead to fatal mission failure. Thus, several methods to minimize the assembly misalignment of missiles have been suggested, including assembly guiding tools and measuring devices. However, previously suggested solutions have disadvantages in versatility and cost. In this study, the low cost and universally applicable solution based on inclinometers for measuring assembly misalignment of a missile is introduced. The comparison between measurement data of the suggested system and a three-dimensional laser tracker for a missile assembly misalignment was conducted. The results show the suggested system can quantify a missile assembly misalignment with comparable precision and accuracy.