The invention provides an alignment method and system for a movable base for an integrated navigation system. The method comprises the steps that firstly, navigation information and GPS observation information are obtained; secondly, an error model for alignment of the movable base is built; thirdly, a Kalman observation controller is built, wherein work of the Kalman observation controller is divided into multiple stages, and each stage corresponds to a state covariance matrix; fourthly, control gains of each stage are calculated through the Kalman observation controller based on the navigation information, the GPS observation information and the error model; fifthly, whether the control gains meet the Lyapunov stability condition or not is judged, if not, the third step is returned, and if yes, a compensation vector is calculated based on the control gains, the compensation vector is fed back to an inertial measurement unit, and the inertial measurement unit performs adjustment. According to the method, by the adoption of the Kalman observation controller, a navigation angle error can be lowered within a quite small range, and therefore alignment time is greatly reduced and alignment precision is improved.