Sony A6400 has a 24.0MP APS-C (23.5 x 15.6 mm ) sized CMOS sensor and features Bionz X processor. On the other hand, Fujifilm X-T3 has a 26.0MP APS-C (23.5 x 15.6 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor.
Another difference between these two cameras is that Fujifilm X-T3'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 X-T3 sensor size comparison.
Sony A6400 and Fujifilm X-T3 have sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Sony A6400 has 8% larger pixel area compared to Fujifilm X-T3, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.