Microburst wind shears (MB) are powerful localized three dimensional (3D) columns of wind that occur when cooled air drops from the base of thunderstorms at high speeds. They eventually hit the ground and spread out in all directions. As such MBs are considered a major atmospheric hazard for aircrafts (ACs), especially in terminal flight phases. Though pilots train regularly to survive it, yet the most recommended practice within the aviation community is to avoid its encounter upon detection. Some modern aircrafts have predictive wind shear warning systems, but they have limited short range capability and do not provide quantitative data for engineering application. In this sense, accurate onboard detection and identification of MBs and its characteristics is of importance for flight safety, whose success can lead to design of automatic flight control systems (FCSs) that reduce the risk of aircraft crash landings and accidents. Even though there are some studies on FCS designs for MB encounter, research on MB identification is rare but ongoing. To this aim, the present study is among the firsts that focuses on online identification of multiple and moving MB parameters using onboard aircraft air data and inertial sensors. The identification task is initially performed using the aircraft six degrees of freedom (6DoF) equations of motion (EOM) integrated with a 3D MB model via the utility of nonlinear Kalman filtering (KF) algorithms. Subsequently, an enhanced neural metaheuristic Kalman filter (NMKF) is proposed that improves the estimation accuracy of the MB model parameters. The results demonstrate the efficacy of the proposed NMKF in comparison with previous studies.