Abstract: Water-soluble pectin was extracted from red-flesh guava peel and pulp by ultrasonic-assisted citric acid extraction. The functional group characteristics, monosaccharide composition, thermal stability, rheological properties, and microstructure of guava pectin were studied. The combination of guava peel pectin and pulp pectin with fat, cholesterol micelle, and cholate were studied in vitro. The esterification degree of guava peel pectin was 56.29%. The average molecular weight had two grades, which were 618.40 kDa (43.4%) and 93.90 kDa (56.6%) individually. Neutral sugar composition: 0.58%±0.02% rhamnose, 0.02%±0.01% petrolatose, 88.48%±0.07% arabinose, 0.78%±0.06% xylose, 0.07%±0.02% mannose, 0.40%±0.03% glucose, 9.68%±0.03% galactose. The esterification degree of guava pulp pectin was 48.57%, and the average molecular weight was 1168.00 kDa (11.0%), 120.30 kDa (53.9%) and 64.94 kDa (35.1%), individually. Neutral sugar composition: 0.47%±0.03% rhamnose, 0.03%±0.01% norvoose, 83.86%±0.04% arabinose, 0.76%±0.05% xylose, 0.08%±0.01% mannose, 0.43%±0.02% glucose, 14.37%±0.05% galactose. The particle size of peel pectin solution was significantly smaller than that of pulp pectin (P<0.05). Both kinds of pectin showed the characteristics of pseudoplastic fluid. At the same concentration, the apparent viscosity of pulp pectin solution was higher than that of peel pectin. There were differences between the two types of pectin, with more tentacle filaments at the edge of the peel pectin and deeper folds in the pulp pectin based on the results from the scanning electron microscope (SEM). The absorption of fat, binding amount of cholesterol micelle and cholic acid by pulp pectin were significantly better than that of peel pectin (P<0.05). These results indicated that both of them had lipid-lowering functions in vitro, and the effect of pulp pectin was better than that of peel pectin. The difference in biological activity resulted from the different molecular structure of the two.