Based on the division of the type and evolutionary phase of Middle and Upper Yangtze cratonic basin in Caledonian Period, this paper has analyzed the sedimentary filling process of typical basin, discussed the filling characteristics of sedimentary sequence and its difference and established the sedimentary evolution model in stages. It is found by the study that the Middle and Upper Yangtze craton in Caledonian Period is composed of two sedimentary system tracts including intracraton and craton-margin and the basin undergoes two evolutionary phases that change from extension mechanism to compression mechanism. In a word, the controlling factors for the filling process of tectonic-sequence are complicated and changeable. Besides, the sedimentary model of each phase has inheritance and divergence characteristics in some aspects. Especially, the Middle and Upper Yangtze craton in Caledonian is characterized by the framework of uplift and depression.