Existing research suggests that lower limb exoskeleton robots, when used for rehabilitation training based on the pre-stroke gait trajectories of stroke patients, may be more beneficial for gait rehabilitation. However, it’s challenging to obtain such personalized trajectories for specific patients. Therefore, this hypothesis is difficult to be verified. This paper introduces an Individualized Gait Trajectory Generation (IGTG) method based on Fast Fourier Transform (FFT) to approximate and regress pre-stroke gaits, along with conducting clinical rehabilitation validation trials. Initially, human gait trajectories are described using Fourier coefficients to construct gait features. Subsequently, a probabilistic mapping between these gait features and physical body parameters is established. Then, personalized gait trajectories are obtained by applying the inverse Fourier transform to the predicted gait features. The application of fast Fourier transform can reduce the number of the regression data points needed, decrease dependency on large datasets, and enhance the systematic robustness. This algorithm is trained using body parameters and gait trajectories collected from 128 healthy subjects. The algorithm is further applied to generate specific personalized trajectories for the 9 stroke patients. Clinical trial results indicate that rehabilitation training using these individualized gait trajectories reduces blood oxygen saturation (SpO2) and heart rate (HR) by up to 66.67% and 69.23% respectively compared to training with fixed trajectories. Note to Practitioners—The main purpose of this paper is to solve gait trajectories mismatch problem when different stroke patients use lower limb exoskeleton robot for rehabilitation training. Variations in body factors among individuals lead to different gait trajectories including walking speed, gender, age, and other anthropometric parameters. Therefore, this paper introduces a novel Individualized Gait Trajectory Generatio...