The Neoproterozoic-Cambrian (N-C) and Permian-Triassic (P-T) transitions have been regarded the two most critical transitions in earth history because of the explosive biological radiation in the early Cambrian (the Cambrian Explosion) and the largest mass extinction at the end-Permian. Previous studies suggest that these two critical transitions showed certain comparability in major evolutionary events. In other words, a series of biological, geological, and geochemical events that had happened in the N-C transition occurred repeatedly during the P-T transition. Those events included continental re-configuration related to the deep mantle dynamics, global-scale glaciations, large C-, Sr-, and S-isotope perturbations indicating atmospheric and oceanic changes, abnormal precipitation of carbonates, and associated multiple biological radiations and mass extinctions. The coupling of those events in both N-C and P-T transitions suggests that deep mantle dynamics could be a primary mechanism driving dramatic changes of environment on the earth's surface, which in turn caused major biological re-organizations. A detailed comparison of those events during the two critical transitions indicates that despite their general comparability, significant differences do exist in magnitude, duration, and frequency. The supercontinent Rodinia began to rift before the Snowball Earth time. By contrast, the supercontinent Pangea entered the dispersal stage after the greatest glaciation from the Late Carboniferous to Cisuralian. Quantitative data and qualitative analyses of different fossil groups show a more profound mass extinction during the N-C transition than at the end-Permian in terms of ecosystem disruption. This is indicated by the disappearance of the whole Ediacaran biota at the N-C boundary. The subsequent appearances of many new complex animals at phylum level in the early Cambrian mark the establishment of a brand new ecosystem. However, the end-Permian mass extinction is manifested mainly by the extinction of many different taxa at class and order levels. Although it caused the extinction of 95% of marine species and 75% of terrestrial species as well as complete cessation of coal and reef deposits after the mass extinction, this high-level biological re-organization still occurred within an established ecosystem, however drastic it may seem. Survived or Lazarus taxa re-occupied the existing ecospace in a relatively short duration after the end-Permian mass extinction. C-isotope excursions display large perturbations during both transitions, yet also in different magnitudes and frequencies, which suggest different atmospheric and oceanic conditions. The recurrent geological and geochemical events as well as the coupled major biological turnovers during the two transitions provide new clues to understanding the interplays among the earth-life system. Thus, it is essential to carry out multidisciplinary studies from the deep internal system to the surface of the Earth as a whole in order to unravel the interactions of dif...