Pentax 645D has a 40.0MP Medium format (44 x 33 mm ) sized CCD sensor and features Prime II processor. On the other hand, Canon 1D X III has a 20.0MP Full frame (36 x 24 mm ) sized CMOS sensor and features Digic X processor.
Pentax 645D's sensor provides 20MP more than Canon 1D X III'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 Pentax 645D'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 645D and 1D X MIII sensor size comparison.
As seen above, Pentax 645D has a 1.7x Larger sensor area than Canon 1D X III. 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.