Saussurea costus (Falc) Lipsch is a traditional herb used to treat kidney stone problems because it contains several molecules used to treat this health problem, such as quercitrin. Infectious stones are the most painful of all urinary tract disorders, with ammonium phosphate (struvite) and carbapatite stones being the most common, caused by a bacterial infection with urease activity. These stones are treated with antibiotics, but antibiotic resistance is on the rise. The current study investigated the anti-urolithic activities of S. costus aqueous and ethanolic extracts of against struvite crystals synthesized using microscopic crystallization and turbidimetric methods, respectively. The utilized methods indicated that the ethanolic extract of this plant has a significant inhibitory effect on struvite crystallization, with a percentage inhibition of (87.45 ± 1.107) (p < 0.001) for a concentration of 1 mg mL−1 and a decrease in the number of struvite crystals, reaching values less than 100/mm3. For the number of struvite crystals inhibited by cystone, we found a value of 400/mm3 and with the aqueous extract we found 700/mm3. The antibacterial activity of the plant extracts studied was examined against several urease-producing bacteria, and this activity was evaluated by qualitative and quantitative evaluation methods; the highest minimum inhibitory concentration was seen in the ethanolic extract, with an MIC of 50 mg mL−1 for Staphylococcus aureus followed by an MIC of 200 mg mL−1 for Klebsiella pneumoniae. It showed a minimal bactericidal concentration (MBC) against S. aureus and K. pneumoniae (>50 mg mL−1 and >200 mg mL−1, respectively). Furthermore, to determine the extract’s anti-inflammatory activity, in vivo anti-inflammatory activity was investigated in rats. The results show that at a dose of 400 mg kg−1, the ethanolic extract has a maximum edema inhibition of 66%.