The primary goal of brain-computer interfaces (BCIs) is to establish a direct linkage between neural activities and behavioral actions via neural decoders. Due to the nonstationary property of neural signals, BCIs trained on one day usually obtain degraded performance on other days, hindering the user experience. Existing studies attempted to address this problem by aligning neural signals across different days. However, these neural adaptation methods may exhibit instability and poor performance when only a few trials are available for alignment, limiting their practicality in real-world BCI deployment. To achieve efficient and stable neural adaptation with few trials, we propose Flow-Based Distribution Alignment (FDA), a novel framework that utilizes flow matching to learn flexible neural representations with stable latent dynamics, thereby facilitating source-free domain alignment through likelihood maximization. The latent dynamics of FDA framework is theoretically proven to be stable using Lyapunov exponents, allowing for robust adaptation. Further experiments across multiple motor cortex datasets demonstrate the superior performance of FDA, achieving reliable results with fewer than five trials. Our FDA approach offers a novel and efficient solution for few-trial neural data adaptation, offering significant potential for improving the long-term viability of real-world BCI applications.