Astragalus polysaccharide (APS) was modified using the Na2SeO3/HNO3 method to obtain selenized APS (Se-APS) with a selenium content of 1.75 mg/g. The structure and physicochemical properties of APS and Se-APS were investigated through transmission electron microscopy-energy dispersive spectroscopy mapping, fourier transform infrared spectroscopy, nuclear magnetic resonance, nano-zetasizer analysis, atomic force microscopy, and scanning electron microscopy. APS and Se-APS did not exhibit toxic effects on human kidney proximal tubular epithelial (HK-2) cells and were able to remove hydroxyl and DPPH radicals, alleviate the damage caused by calcium oxalate (CaOx) monohydrate (COM) crystals to HK-2 cells, reduce intracellular reactive oxygen species levels, and restore cell viability and morphology. Both APS and Se-APS could inhibit COM growth, induce calcium oxalate dihydrate formation, and increase the absolute zeta potential of the crystals to inhibit crystal aggregation. However, the ability of Se-APS to regulate CaOx crystals and protect the cells from COM-induced damage was better than that of APS. These results suggested that Se-APS might be a candidate drug for the treatment and prevention of kidney stones.