The Great Ordovician Biodiversification Event (GOBE) introduced both dramatic increase in taxonomic diversity and the complexity of community structure in the marine realm. However, relative few works have assessed comprehensively the changes of sedimentary systems in shallow-marine settings responding to the GOBE. Data presented here illustrate that the sedimentary systems on the South China and North China paleoplates changed markedly as a consequence of the first major phase of the Ordovician biodiversification. Pre-GOBE sedimentary systems in the Tremadocian display widespread microbialites and flat-pebble conglomerates and the indigent extent of bioturbation. Through the transitional period of the early Floian, the sedimentary system in the rest of the Early and Mid Ordovician changes to GOBE-type, characterized by intensive bioturbation and vanishing flat-pebble conglomerate and subtidal microbial sediment. The irreversible changes in the sedimentary systems in North and South China may be a consequence of the Ordovician biodiversification instead of its environmental background. Further detailed and quantitative field studies on the changes in sedimentary systems are crucial for understanding the ultimate causes of the GOBE.