Micro Measurement and Flight Control System (MMFCS) is important for an autonomous Micro Aerial Vehicle (MAV) to accomplish a flight task. Being in small size, low speed and limited payload capacity, most conventional measurement and control system is no longer practical in Micro Aerial Vehicle (MAV). In this paper presents a study on micro-MMFCS system based on criteria of minimum size and low computational complexity to complete the autonomous fly. Via using MEMS sensors, the developed micro MMFCS is with a size of 65×40×12mm3 and a weight of 22g. A novel linear fusion algorithm with a linear (and simple) Kalman model is presented to get the roll and pitch angle, then, the controller is designed in the lateral and longitudinal control loop for the trajectory tracking. Examples of waypoint-based autonomous fly mission, using the micro-MMFCS system of a MAV with a wingspan of 380 mm, is presented, with the results demonstrate the effectiveness of the proposed system.