DOA (Direction of Arrival), as an important observation parameter for accurately locating the Signals of Opportunity (SOP), is vital for navigation in GNSS-challenged environments and can be effectively obtained through sparse arrays. In practical application, array perturbations affect the estimation accuracy and stability of DOA, thereby adversely affecting the positioning performance of SOP. Against this backdrop, we propose an approach to reconstruct non-uniform arrays under perturbation conditions, aiming to improve the robustness of DOA estimation in sparse arrays. Firstly, we theoretically derive the mathematical expressions of the Cramér–Rao Bound (CRB) and Spatial Correlation Coefficient (SCC) for the uniform linear array (ULA) with perturbation. Then, we minimize CRB as the objective function to mitigate the adverse effects of array perturbations on DOA estimation, and use SCC as a constraint to suppress sidelobes. By doing this, the non-uniform array reconstruction model is formulated as a high-order 0–1 optimization problem. To effectively solve this nonconvex model, we propose a polynomial-time algorithm, which can converge to the optimal approximate solution of the original model. Finally, through a series of simulation experiments utilizing frequency modulation (FM) signal as an example, the exceptional performance of this method in array reconstruction has been thoroughly validated. Experimental data show that the reconstructed non-uniform array excels in DOA estimation accuracy compared to other sparse arrays, making it particularly suitable for estimating the direction of terrestrial SOP in perturbed environments.