Owing to the low contents of their acid-insoluble components, carbonate rocks tend to decrease sharply in volume in association with the formation of weathering crust. The formation of a 1 m-thick weathering crust would usually consume more than ten meters to several tens of meters of thickness of parent rocks. The knowledge of how to identify the homogeneity of parent rocks is essential to understand the formation mechanism of weathering crust in karst regions, especially that of thick-layered red weathering crust. In this work the grain-size analyses have demonstrated that the three profiles studied are the residual weathering crust of carbonate rocks and further showed that there objectively exists the heterogeneity of parent rocks in the three studied weathering crusts. The heterogeneity of parent rocks can also be reflected m geochemical parameters of major elements, just as the characteristics of frequency plot of grain-size distribution. Conservative trace element ratios Zr/Hf and Nb/Ta are proven to be unsuitable for tracing the heterogeneity of parent rocks of weathering crust, but its geochemical mechanism is unclear. The authors strongly suggest in this paper that the identification of the homogeneity of parent rocks of weathering crust in karst regions is of prime necessity.