A chromatic confocal microscope system and signal process method is provided to utilize a first optical fiber module for modulating a light into a detecting light passing through a chromatic dispersion objective and thereby forming a plurality of chromatic dispersion lights to project onto an object. A second optical fiber module conjugated with the first optical fiber module receives a reflected object light for forming a filtered light, which is split into two filtered lights detected by two color sensing units for generating two sets of RGB intensity signals, wherein one set of RGB intensity signals is adjusted relative to the other set of RGB intensity signals. Then two sets of RGB intensity signals are calculated for obtaining a maximum ratio factor. Finally, according to the maximum ratio factor and a depth relation curve, the surface profile of the object can be reconstructed.