Face detection often plays the first step in various visual applications. Large variants of facial deformations due to head movements and facial expression make it difficult to identify appropriate face region. In this paper, a robust real-time face alignment system, including facial landmarks detection and face rectification, is proposed. A facial landmarks detection model based on regression tree is utilized in the proposed system. In face rectification framework, 2-D geometrical analysis based on pitch, yaw and roll movements is designed to solve the misalignment problem in face detection. The experiments on the two datasets verify the performance significantly improved by the proposed method in the facial recognition task and outperform than those obtained by other alignment methods. Furthermore, the proposed method can achieve robust recognition results even if the amount of training images is not large.