Fujifilm S1 Pro has a 3.0MP APS-C (23 x 15.5 mm ) sized CCD sensor . On the other hand, Canon 1D X II has a 20.0MP Full frame (36 x 24 mm ) sized CMOS sensor and features Dual DIGIC 6+ processor. Canon 1D X II's sensor provides 17MP more than Fujifilm S1 Pro'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 S1 Pro and 1D X MII sensor size comparison.
As seen above, Canon 1D X II has a 2.4x Larger sensor area than Fujifilm S1 Pro. 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.