Both Sony A6400 and Sony A9 have 24.0 MP resolution sensors but Sony A6400's sensor is APS-C (23.5 x 15.6 mm ) and Sony A9's sensor is Full frame (35.6 x 23.8 mm ).
Since Sony A9's has a larger sensor area with the same resolution, this means that it also has a larger pixel area hence better light collecting capacity for a given aperture compared to Sony A6400.
Another difference between these two cameras is that Sony A9's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the A6400 and A9 sensor size comparison.
As seen above, Sony A9 has a 2.3x Larger sensor area than Sony A6400. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.