Sony A6600 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 X-Trans CMOS 4 sensor and features X-Processor 4 processor.
One other difference between these two cameras that is worth mentioning is that Fujifilm X-T3'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 A6600 and X-T3 sensor size comparison.
Sony A6600 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 A6600 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.