The advancement of microbiome technologies has facilitated a growing interest in the interactions between urinary microbiota and urinary stone formation. This article systematically reviews the technological evolution, and the reciprocal mechanism of microbiota involvement in lithogenesis and its clinical significance. It specifically highlights the changes within the urinary microbiota of calcium oxalate stone patients, notably a depletion of Lactobacillus populations and an enrichment of pathogenic taxa such as Enterobacteriaceae. Furthermore, it delineates the mechanisms whereby microbes participate in stone formation through metabolic regulation, physical adhesion, and inflammatory processes. The article also explores the influence exerted by distinct stone types on the structural composition and functional dynamics of the urinary microbiota. Integrated multi-omics analyses offer novel perspectives for unraveling the intricate microbiome-host interaction network. This approach is anticipated to facilitate significant advances in developing precision-focused prophylactic and therapeutic strategies for urinary stones from a microecological standpoint.