Early warnings for dynamical transitions in complex systems or high-dimensional observation data are essential in many real world applications, such as gene mutation, brain diseases, natural disasters, financial crises, and engineering reliability. To effectively extract early warning signals, we develop a novel approach: the directed anisotropic diffusion map that captures the latent evolutionary dynamics in low-dimensional manifold. Applying the methodology to authentic electroencephalogram (EEG) data, we successfully find the appropriate effective coordinates, and derive early warning signals capable of detecting the tipping point during the state transition. Our method bridges the latent dynamics with the original dataset. The framework is validated to be accurate and effective through numerical experiments, in terms of density and transition probability. It is shown that the second coordinate holds meaningful information for critical transition in various evaluation metrics.