Future aerospace vehicles (ASV) are designed to fly in both inner and extra atmospheric fields, which requires autonomous adaptability to the uncertainties emanated from abrupt faults and continuously time-varying environments. An autonomous control reconfiguration scheme is presented for ASV to deal with the uncertainties on the base of control effectiveness estimation. The on-line estimation methods for the time-varying control effectiveness of linear control system are investigated. Some sufficient conditions for the estimable system are given for different cases. There are proposed corresponding on-line estimation algorithms which are proved to be convergent and robust to noise using the least-square-based methods. On the ground of fuzzy logic and linear programming, the control allocation algorithms, which are able to implement the autonomous control reconfiguration through the redundant actuators, are put forward. Finally, an integrated system is developed to verify the scheme and algorithms by way of numerical simulation and analysis.