Fujifilm X-Pro3 has a 26.0MP APS-C (23.5 x 15.6 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor. On the other hand, Fujifilm GFX 100S has a 102.0MP Medium format (44 x 33 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor.
Fujifilm GFX 100S's sensor provides 76MP more than Fujifilm X-Pro3's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Another difference between these two cameras is that Fujifilm X-Pro3'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-Pro3 and GFX 100S sensor size comparison.
As seen above, Fujifilm GFX 100S has a 4.0x Larger sensor area than Fujifilm X-Pro3. 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.