Both GC-MS and RNA-Seq were employed to investigate the changes in volatile compounds and expression pattern of genes involved in biosynthesis pathway of terpenoid in the pulp of Ponkan fruit during section-drying process. The results were as follows: ① 13 volatile components were identified from pulp of Ponkan fruit, among which seven components were terpenoid, accounting for more than 85% of the total volatile contents. ② The volatile constituents in pup were same between normal and disordered fruits. In fruits affected by section-drying, the content of total volatiles and terpenoid decreased to 32% and 22%, respectively, of normal fruits. A total of five volatiles including β-myrcene, d-limonene, γ-terpinene, valencene and dodecanal showed a significant decrease in content during the section-drying process. ③ Eight differentially expressed genes involved in terpenoid biosynthesis pathway were identified, all of which were decreased in disordered fruits. The present study elucidated that the volatile constituents in pulp of Ponkan fruits decreased upon section-drying, which was quite closely related to the decreasing expression of genes involved in terpenoid synthesis. Moreover, this study provided invaluable information for further research to reveal the molecular mechanism underlying section-drying in citrus fruits.