To reduce downstream rework and design changes, variation modeling and analysis are indispensable in the assembly of complex products. In this paper, a rigid-compliant hybrid variation analysis method using the Monte Carlo interval approach is developed to assembly ladder structures, such as the skeleton of a horizontal stabilizer or a wing box. We first present the classical locating scheme of a low-rigidity aeronautical structure, and the contributors to the assembly variation of a ladder structure comprising locating errors and part geometric errors. Assembly variations induced by rigid-body locating errors and part geometric errors are mathematically modeled with rigid-body kinematics and the mechanistic method based on the Finite Element Analysis, respectively. And then, the two types of assembly variations are integrated into a rigid-compliant hybrid variation model. Probability distributions of the contributors are often unknown, especially in aircraft manufacturing with low production volume. Therefore, a novel variation analysis method using the Monte Carlo interval approach is proposed to compute the assembly variation, represented in the form of interval structural parameters. The assembly case of a scale wing skeleton shows the proposed rigid-compliant hybrid variation analysis method is efficient in the assembly variation analysis for low-rigidity aircraft structure.