Canon M3 has a 24.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features DIGIC 6 processor. On the other hand, Fujifilm GFX 100 has a 102.0MP Medium format (44 x 33 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor.
Fujifilm GFX 100's sensor provides 78MP more than Canon M3'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.
Below you can see the M3 and GFX 100 sensor size comparison.
As seen above, Fujifilm GFX 100 has a 4.4x Larger sensor area than Canon M3. 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.