Terpenoids are the largest and most diverse class of plant specialized metabolites, which function in diverse physiological processes during plant development. In the biosynthesis of plant terpenoids, short-chain prenyltransferase (SC-PT), together with terpene synthase (TPS), play a role in determining terpenoid diversity. SC-PTs biosynthesize prenyl pyrophosphates with different chain lengths and these compounds are the direct precursors of terpenoids. Arabidopsis thaliana possesses a subgroup of SC-PTs whose functions are not clearly known (we focus on 10 geranylgeranyl pyrophosphate synthase-like (GGPPSL) proteins here, which are commonly thought to produce GGPP [C20]). In this study, we find that a subset members of the Arabidopsis GGPPSL gene family have undergone neo-functionalization: GGPPSL6, 7, 9, and 10 mainly have geranylfarnesyl pyrophosphate synthase activity ([C25]; renamed as AtGFPPS1, 2, 3 and 4), and GGPPSL8 produces even longer chain prenyl pyrophosphate (≥ C30, renamed as polyprenyl pyrophosphate synthase 2, AtPPPS2). By solving the crystal structures of AtGFPPS2, AtPPPS2 and AtGGPPS11, we reveal the product chain-length determination mechanism of SC-PTs and describe it as a “three floors” model. Using this model, we identified a novel GFPPS clade distributed in Brassicaceae plants. In addition, we find that the GFPPS gene typically occurs in tandem with a gene encoding a TPS, forming a GFPPS-TPS gene cluster.