In the assembly process of large-size aerospace products, the leveling and horizontal alignment of large components are essential prior to the installation of an inertial navigation system (INS) and the final quality inspection. In general, the inherent coordinate systems of large-scale coordinate measuring devices are not coincident with the geodetic horizontal system, and a dualaxis compensation system is commonly required for the measurement of difference in heights. These compensation systems are expensive and dedicated designs for different devices at present. Considering that a large-size assembly site usually needs more than one measuring device, a compensation approach which is versatile for different devices would be a more convenient and economic choice for manufacturers. In this paper, a flexible and cost-effective compensation method is proposed. Firstly, an auxiliary measuring device called a versatile compensation fixture (VCF) is designed, which mainly comprises reference points for coordinate transformation and a dual-axis inclinometer, and a kind of network tighten points (NTPs) are introduced and temporarily deployed in the large measuring space to further reduce transformation error. Secondly, the measuring principle of height difference is studied, based on coordinate transformation theory and trigonometry while considering the effects of earth curvature, and the coordinate transformation parameters are derived by least squares adjustment. Thirdly, the analytical solution of leveling uncertainty is analyzed, based on which the key parameters of the VCF and the proper deployment of NTPs are determined according to the leveling accuracy requirement. Furthermore, the proposed method is practically applied to the assembly of a large helicopter by developing an automatic leveling and alignment system. By measuring four NTPs, the leveling uncertainty (2σ) is reduced by 29.4% to about 0.12 mm, compared with that without NTPs.