Kidney stones are a common urological disease worldwide, imposing a significant burden on healthcare systems. Calcium oxalate stones are the predominant form of urinary calculi, with two main theoretical models explaining their pathogenesis: the fixed particle and free particle models. Regardless of the model, the formation of calcium oxalate kidney stones is inseparably linked to crystal nucleation, growth, aggregation, and adhesion in urine. Growing evidence highlights the significant role of urinary proteins, particularly matrix proteins, in the development of calcium oxalate stones. The review classifies urinary proteins impacting calcium oxalate stone formation into three groups: inhibitors, promoters, and dual-regulators, outlining their contributions to the formation process.