The reflector panel used for a large-scale compact test range (CTR) is usually divided into several sub-panels with appropriate size to be fabricated separately, and then these sub-panels are assembled and aligned for a long period to form a high-precision reflective surface. Toward that end, an iterative alignment system is established to accomplish alignment of reflector panels based on commercial laser tracker and 6-degree-of-freedom adjustment mechanism. The alignment is a very challenging task involving two aspects: coordinate system alignment and measurement uncertainty evaluation, especially in a non-metrology environment. For the former, an alignment method is developed to unify the measurement coordinate system of the system based on iteratively adding and modifying reference points. For the latter, the actual uncertainty model of laser tracker based on a large amount of field measurement data is analyzed and established using statistical analysis. Based on the uncertainty model, the measurement and alignment error is evaluated and verified by Monte Carlo simulations. As verification, 15 sub-panels of the CTR reflector with 12 m width and 7 m height are opportunely assembled and aligned using the iterative alignment system and algorithm. The final root-mean-square error of the deviation between the actual and theoretical profiles is achieved at 0.041 mm, where the accuracy loss caused by alignment is only 7.9% of the theoretical value. Results show that the alignment system and method proposed in this paper is effective and efficient to align the reflector panels for large-scale CTR in a non-metrology environment.