Both Nikon S3300 and Fujifilm X100S have 16.0 MP resolution sensors but Nikon S3300's sensor is 1/2.3-inch (6.17 x 4.55 mm ) and Fujifilm X100S's sensor is APS-C (23.6 x 15.8 mm ).
Since Fujifilm X100S'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 Nikon S3300.
One other difference between these two cameras that is worth mentioning is that Fujifilm X100S'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 moiré occurring in certain scenes.
Below you can see the S3300 and X100S sensor size comparison.
As seen above, Fujifilm X100S has a 13.3x Larger sensor area than Nikon S3300. 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.