Both Fujifilm X-T3 and Canon 6D MII have 26.0 MP resolution sensors but Fujifilm X-T3's sensor is APS-C (23.5 x 15.6 mm ) and Canon 6D MII's sensor is Full frame (35.9 x 24 mm ).
Since Canon 6D MII'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 Fujifilm X-T3.
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 X-T3 and 6D MII sensor size comparison.
As seen above, Canon 6D MII has a 2.4x Larger sensor area than Fujifilm X-T3. 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.