Abstract: Provided in the present invention is a pharmaceutically active ingredient extract extracted from Polygala japonica Houtt., which extract comprises a flavonol compound of the following formula (I) structure as a first active ingredient, and optionally comprises a xanthone compound selected from the following formula (II) as a second active ingredient and a glycolipid compound selected from the following formula (III-1) as a third active ingredient. An animal experiment confirms that the drug of the present invention has significantly better effects than potassium sodium hydrogen citrate in typical test indicators such as calcium oxalate crystal aggregation, renal interstitial inflammatory cell infiltration and renal tubule dilation lesions, showing that the drug has high potential and market prospects in the treatment of urolithiasis and urinary tract infections or kidney damage caused by urolithiasis, and as an adjuvant drug after surgical treatment of urolithiasis.