To deal with the difficulties in predicting elastic deformation of aircraft wrings during the flight, a distributed inertial navigation method for wing deformation measurement is proposed. First, the layout optimization of the critical test points on the wing is conducted based on the modal analysis and the thin plate model combined with the particle swarm optimization algorithm. Second, a relative motion inertial navigation calculating method is proposed by establishing the federated Kalman filter model for the estimation of the relative inertial navigation error. It achieves real-time alignment of each node under wing flexure deformation. Then, wing deformation is described by the positional information of multiple sub-nodes simultaneously. Finally, a wing loading test is conducted to verify the accuracy and effectiveness of the algorithm. The results show that the root means squares (RMSs) of the wing's three-directional position are 0.534 mm, 0.547 mm, 0.451 mm, respectively, and the RMSs of the wing's three-directional posture are 0.772', 2.87', 0.541', respectively. The results demonstrate that the proposed method has high estimation accuracy and good deformation monitoring ability in a dynamic environment.