Non-extractable polyphenol (NEPP) was extracted from the residue of post-citrus polyphenols by high intensity pulsed electric field (PEF). On the basis of single-factor experimental investigation (field intensity, pulse number and liquid to solid ratio, etc.), MTT assay, neutral red colorimetric assay, and Griess assay were used to evaluate the effects of NEPP on the growth, phagocytic activity, and NO release of RAW 264.7 cells. The results showed that the obtained process regression model of kumquat NEPP was significant with great fitting, which predicted the maximum theoretical value of kumquat NEPP content was 1.756 mg/g DW. The optimized NEPP extraction condition of kumquat by PEF was shown as follows: pulse number 450 times, field intensity 11.86 kV/cm, liquid to solid ratio V (water): M (fruit residue) = 0.341 mL: 1mg. Following the optimized extraction method, the NEPP content of kumquat (1.5 mg/g DW) was close to the predicted value, indicating that the optimized PEF process was acceptable to the extraction of kumquat NEPP. Kumquat NEPP (100 g/mL) showed no toxicity to RAW 264.7 macrophages, increased NO secretion and boomed phagocytic activity.