In this paper, we propose a model-based control system design for autonomous flight and guidance control of a small-scale unmanned helicopter. Small-scale unmanned helicopters have been studied by way of fuzzy and neural network theory, but control that is not based on a model fails to yield good stabilization performance. For this reason, we design a mathematical model and a model-based controller for a small-scale unmanned helicopter system. In order to realize a fully autonomous small-scale unmanned helicopter, we have designed a MIMO attitude controller and a trajectory controller equipped with a Kalman filter-based LQI for a small-scale unmanned helicopter. The design of the trajectory controller takes into consideration the characteristics of attitude closed-loop dynamics. Simulations and experiments have shown that the proposed scheme for attitude control and position control is very useful.