The main aim of this paper is to model and simulate flight dynamics and to design a controller for a dragonfly-like micro aerial vehicle (MAV). This MAV has flapping wings using a clap and fling mechanism with a rigid abdomen. Kane’s method is applied to derive the longitudinal motion equations of the MAV as a multi-body system. Then, the aerodynamic lift and drag forces of the MAV are obtained. These equations are substituted in the derived motion equations. Furthermore, a new structure for a dragonfly-like flapping wing MAV is presented in which abdomen motion is considered in the longitudinal mode. In this work, the use of the abdomen is also formulated. A change in the motor’s speed generates differential thrust that creates a pitch moment as a control input. State space linearized equations of motion are presented by using appropriate assumptions in the aerodynamics, and dynamic nonlinear equations. To validate the linearized model, the response of the open-loop linear system is compared with the nonlinear one. In addition, the positive role of the abdomen in the open loop is discussed and analyzed. Finally, an LQR controller is designed for the pitch mode which is robust against disturbances. The validity, effectiveness, and performance of the derived equations and designed autopilot are shown by implemented hardware in the loop testbed using a fixed abdomen. Results demonstrate a good agreement between theoretical and experimental responses with accurate hovering at the desired angle.