This research work is a part of a research project funded by Defense Science Organisation (DSO) to develop a vertical takeoff and landing (VTOL) micro air vehicle (MAV). Previous work has focused on conceptual design and numerical investigation of the aerodynamic properties of the MAV. This work focuses on the dynamic analysis and control system design of the current MAV design during non-hover flight. Both numerical simulation and analytical approaches were employed to obtain the results. For the simulation approach, a full 6 degree-of-freedom model was built using MATLAB Simulink and Aerospace Blockset. The design of the flight control system was based on the linearised mathematical model of the MAV. Based on this linear model, appropriate control strategies were developed for various flight conditions such as cruise, climb, and turning flight. Finally, the controllers developed based on the linear approximation were applied to the non-linear system to examine their validity. It was proven that the designed controllers worked well for the non-linear aircraft model, even in the presence of disturbances. Finally, preliminary implementation of the embedded control system, which consists of an Inertial Measurement Unit (IMU) and a servo control board, to the MAV prototype was developed.