This paper reports on measurement method of aerodynamic force of a fruit fly (Drosophila) during flapping motion using a MEMS (Micro Electro Mechanical Systems) multi axis force sensor. The proposed MEMS multi axis force sensor is composed of a Si probe and supported beams whose surface or sidewall area is doped to measure 3 axis forces and moment around the probe. The sensor size is approximately 1800 μm × 2800 μm × 35 μm. The force and moment resolution are designed to be under 1 μN and 1.0 μNm, respectively. The aerodynamic force vector can be detected by attaching a fruit fly to the tip of the probe. Using the fabricated force sensor, we developed sensor attachment setup and experimental setup to measure aerodynamic force of a fruit fly.