The purpose of this study is to understand the effect of cross flow and fluctuating flow on the propeller performance of MAV. This study especially has focused on the propeller performance during hovering flight under several cross flow velocity in actual flight conditions. We investigated four test cases of propellers with different starting point of design. The thrust and the torque of each propeller were experimentally measured by using the force transducer in wind tunnel. Figure of Merit (FM) of each propeller were evaluated based on the thrust and the torque measurement. The results showed that low cross flow velocity reduced FM. However, high cross flow velocity improved FM. Fluctuating flow yielded the change of FM with time. Furthermore, it was found that the starting point of the propeller design had a great effect on FM under wind environments.