In this study, pectin was modified with ferulic acid (Fa), trans-ferulic acid (trans-Fa), methyl gallate (MG), and ethyl gallate (EG) via the enzymatic method using aqueous/organic phases to enhance its physiochemical and bio-active properties. Results revealed that lipase might catalyze the hydrolysis of the ester bond within pectin in aqueous phase and prompt the transesterification between the hydroxyl group in the para position in Fa/trans-Fa or the 2′-OH group of MG/EG and the carboxylic group of pectin in the organic phase.The graft ratio was 21.00%, 21.67%, 13.24%, and 11.93% for the Fa-, trans-Fa-, MG-, and EG-modified pectin, respectively. In addition, compared with native pectin, the modified pectin exhibited improved apparent viscosity and emulsion activity. Moreover, the clearance of 1,1-diphenyl-2-picryl hydrazine (DPPH) and 2,2′-azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) was effectively enhanced for the modified pectin. Furthermore, the modified pectin exhibited strong antibacterial activity against Escherichia coli and Staphylococcus aureus while no cytotoxic effects based on the results of cell culture experiments. Our results provide a theoretical basis for the expansion of pectin applications in the food and pharmaceutical industries.