Premma puberula Pamp. is a kind of medicinal and edible plant that is widely distributed in Southwest of China. The content of pectin in different tissues is different, but the reason for the difference is unknown. In this study, we detected and found that pectin content varies greatly in roots, stems and leaves of P. puberula and we carried out microstructure of leaves, stems and roots, detected histochemical localization, galacturonic acid (GalA) content, degree of esterification (DE), scanning electron microscopy (SEM), X-ray diffraction (XRD) of pectin and binding transcriptomics to investigate the pectin polysaccharide biosynthesis and related genes from different tissues at the molecular level. A total of 26.04 Gb clean data of the high-quality reads were successfully mapped to the reference genome of P. puberula and assembled into 107,250 nonredundant genes. We mapped all of the genes to reference pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to identify pectin biosynthesis pathways in which the genes might be involved, which provide understanding of the regulation of P. puberula pectin at the molecular level. The pectin-related key enzyme genes were identified, and these studies have important value for understanding the biosynthesis mechanism of pectin in different tissues.