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.
One other difference between these two cameras that is worth mentioning is that Sony A9's sensor doesn't have an 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.
DxOMark Sensor Scores
DxOMark is a benchmark that scientifically assesses image quality of camera sensors. It scores camera sensors for color depth (DXO Portrait), dynamic range (DXO Landscape) and low-light sensitivity (DXO Sports), and also gives them an overall score. Sony A6400 and Sony A9 sensors have been tested by DxO and the results show that A9 has a better overall score of 92, 9 points higher compared to A6400's score of 83.