Performance of the existing physical layer authentication schemes could be severely affected by the imperfect estimates and variations of the communication link attributes used. The commonly adopted static hypothesis testing for physical layer authentication faces significant challenges in time-varying communication channels due to the changing propagation and interference conditions, which are typically unknown at the design stage. To circumvent this impediment, we propose an adaptive physical layer authentication scheme based on machine-learning as an intelligent process to learn and utilize the complex and time-varying environment, and hence to improve the reliability and robustness of physical layer authentication. Explicitly, a physical layer attribute fusion model based on a kernel machine is designed for dealing with multiple attributes without requiring the knowledge of their statistical properties. By modeling the physical layer authentication as a linear system, the proposed technique directly reduces the authentication scope from a combined N-dimensional feature space to a single dimensional (scalar) space, hence leading to reduced authentication complexity. By formulating the learning (training) objective of the physical layer authentication as a convex problem, an adaptive algorithm based on kernel least-mean-square is then proposed as an intelligent process to learn and track the variations of multiple attributes, and therefore to enhance the authentication performance. Both the convergence and the authentication performance of the proposed intelligent authentication process are theoretically analyzed. Our simulations demonstrate that our solution significantly improves the authentication performance in time-varying environments.