Space Situational Awareness (SSA) has been recognized to be important for safe space activities. As low-thrust propulsion technology becomes increasingly popular, SSA for low-thrust spacecraft may become an area of increasing interest. In this paper, we propose an orbital estimation method to predict the long-term evolution of spacecraft trajectory under unknown low-thrust acceleration. In particular, by the use of the perturbation theory and a nonlinear Kalman filter, long-term variations of orbital elements and thrust accelerations can be estimated from observation data of mean orbital elements. Performance of our method are evaluated for both controlled and uncontrolled orbits.