Modern aircraft such as missile and rocket, due to the large slenderness ratio of slender body vehicles, the influence of elastic deformation and vibration on navigation, guidance, and engine modules in simulation can not be ignored. For the problems of slow calculation speed and incapability of real-time simulation for time-domain simulation, by analyzing the time proportion of each calculation step under different computing scale, the dynamic parallel construction of octree is used to represent the aerodynamic parameter table under the environment of single and multi GPU. Meanwhile, an innovative parallel algorithm of element stiffness matrix based on finite element model is designed in GPU architecture. Accordingly, the optimized performance is enhanced through the adaptive hardware resources and rational use of shared memory. Furthermore, A multi-threaded asynchronous framework based on task queue and thread pool is proposed to realize the parallel task calculation with different granularities. The numerical result shows that the acceleration ratio of about 20 times in the single GPU condition can be obtained, and the acceleration ratio of at least 30 times can be obtained by the parallel computing of dual GPUs, enabling the real-time simulation of the flexible aircraft with 1200 elements within 20ms. INDEX TERMS Flexible aircraft, parallel computing, parallel algorithms, heterogeneous computing, Octree.