A square root based spherical simplex unscented transform was adopted in micro satellite attitude determination filter. The filter computation cost was reduced evidently by means of spherical simplex unscented transformation (SSUT) and the square root technique with modified Rodrigues parameters (MRPs). The filter performance and numerical stability were guaranteed by unscented transformation with positive-semi definiteness of the state covariance propagation. The simulation results of some micro-satellite showed that this algorithm could insure accuracy, fast convergence and high robustness with high computation efficiency, which was suitable for the attitude estimation of micro-satellite.