A large aircraft fuselage panel is commonly composed of a variety of thin-walled components. Most of these components are large, thin and compliant, and they are also prone to some flexible deformation during assembly and remain deformed after assembly. Besides, many different fabrication and assembly manners are adopted in order to guarantee the complicated assembly relationships between each component. The above characteristics often cause large aircraft fuselage panels to exhibit low stiffness and weak strength, thereby inducing deformation during assembly. Since the posture of a large aircraft fuselage panel is commonly evaluated by matching the theoretical and actual positions of the measurement points placed on it, and its assembly deformation is also represented by the position errors of the measurement points, a reasonable measurement point placement is significant for the large aircraft fuselage panel in digital assembly. This article presents a method based on the D-optimality method and the adaptive simulated annealing genetic algorithm to optimize the placement of the measurement points which can cover more deformation information of the panel for effective assembly error diagnosis. By taking the principle of the D-optimality method, an optimal set of measurement points is selected from a larger candidate set through adaptive simulated annealing genetic algorithm. As illustrated by an example, the final measurement point configuration is more effective to maximize the determinant of the corresponding Fisher Information Matrix and minimize the estimation error of the assembly deformation than those obtained by other methods.