Statistical analysis based on global data indicated that the planktonic graptolites presented a distinguished pattern from that of benthic communities during the great Ordovician biodiversification. The graptolites started to diversify from the beginning of Ordovician and reached an acme in the early Middle Ordovician, but subsequently underwent a steady decline to the end of Ordovician. During the Ordovician, many clades of the graptolites made their originations, flourishing and replacements. However, in different regions and distinct environments across the world, graptolites may presumably display distinct patterns of radiation and evolution, a hypothesis to be tested. Herein a study of the graptolite diversity in the Early to Middle Ordovician in the Upper Yangtze Region (Platform) and Jiangnan Region (Slope), South China, is conducted. The results indicate that graptolites underwent a remarkable increase in both regions, but with distinct magnitude, scope, process and patterns. The diversification of graptolites in the Upper Yangtze Region, though less prominent, is divided into four stages and includes two peaks. In the Jiangnan Region, the graptolite diversification is far more prominent and includes three stages and one peak. Based on the distinct diversity histories and composition of graptolites in the two representative regions, a ‘deep-water origin and shallow-water dispersal’ model is proposed for the Ordovician graptolite faunas. According to the model, the major graptolite faunas of Ordovician originated in the deep-water region on the continental slope, the source of the graptolite novelties, and subsequently spread into shallow-water region on the shelf. Besides, we also conduct a comparison study of the Ordovician graptolite diversity in South China and other major regions. The results display that the graptolites diversified globally in the Early and Middle Ordovician. At the beginning of Ordovician, graptolites underwent a significant ecological innovation of graptolites: planktonic forms were derived from their benthic ancestors. This derivation resulted in the great guild expansion of graptolites. In late Early Ordovician (Floian), the global expansion of graptolites commenced. From the Floian to the end of Middle Ordovician, the graptolites diversity increased remarkably and displayed three peaks for all the regions. However, the peaks are somewhat distinct in magnitude and timing among regions. The Darriwilian peak is prominent in both South China and Baltic region, but inconspicuous in Australasia. No close relationship between the graptolite diversification and the palaeolatitudes are supported herein. Instead, the graptolite diversification seems to coincide with the global sea-level rises, suggesting a possible intrinsic relationship between them.