Flapping wing micro aerial vehicles (FWMAVs) are known for their flight agility and maneuverability. However, their in-gust flight performance and stability is still inferior to their biological counterparts. To this end, a simplified in-gust dynamic model, which could capture the main gust effects on FWMAVs, has been identified with real in-gust flights' data of a FWMAV, the Flapper Drone. Based on this model, an adaptive position and velocity controller was proposed with gain scheduling and implemented for in-gust flights under gust speeds up to 2.4 m/s. With this airflow-sensing based adaptive controller, the in-gust hovering stability of the Flapper Drone has been improved when the gust's intensity and frequency changes, comparing with the original fixed-gain cascaded PID controller case.