Considering of power, size and cost of micro-satellite, MEMS gyroscope, sun sensor and magnetometer are chosen as attitude sensors. In this paper, a Federated Kalman Filter, consisting of two sub-filters and one master filter, is designed to estimate micro-satellite’s attitude. Simulation shows that it performs well and has a better accuracy when compared to traditional method of Runge-Kutta. Besides, it has less calculation load and good fault tolerance which is significant for micro-satellite application.