The invention relates to a microscopic surgical operation navigation system based on augmented reality and a navigation method. The navigation system comprises a fixing frame, a graph mark, a camera, a controller and display equipment, wherein the fixing frame comprises a foundation, a connection member, a fixing rod and a supporting board. The navigation method comprises steps that, S1, the fixing frame is fixed on an ill body; S2, the fixing frame and the ill body are scanned through a CTA, and a three-dimensional model is reconstructed; S3, a three-dimensional coordinate of the three-dimensional model is adjusted through software 3ds MAX to make the graph mark be at the world coordinate center; and S4, the three-dimensional model is projected by ARToolkit software onto a right center of the graph mark, so the three-dimensional model and the ill body image are superposed and fused. The system and the method are advantaged in that, the augmented reality technology is utilized, so the real world information, namely the ill body, is superposed and fused with virtual world information, namely the three-dimensional model of blood vessel muscle bones, so entity information which is difficult to experience in the real world can be acquired by operation doctors.