We constructed a whole of Spermatophyta timetree by employing BEAST v1. X applying the nuclear ribosomal ITS, and chloroplastic matK and rbcL. Robust multipoint calibrations were done by applying fossil ages up to the Jurassic for 20 genera and a Quaternary geological event age of 1.55 Ma for 6 genera. The resultant topology was concordant to the APG system, and we successfully and precisely dated the phylogeny. Through the BEAST analyses, we discovered the exponential increase in base substitution rate in recent geologic time, and suggested that a potential cause was generation of C4 plants and the triggered Quaternary climatic change. The raised rate might have resulted in the increasing of Spermatophyta diversity including endemic Asarum and Viola species. Another rise of base substitution rate was found around 120 Ma, reflecting the order level radiation and diversification of Angiospermae at the middle Cretaceous time.