Bilateral upper urinary tract stones are significantly related to renal function damage. However, few studies characterized the risk factors of bilateral upper urinary tract stones. We retrospectively enrolled 3905 patients with urinary tract stones from March 2019 to March 2022 at the Second Hospital of Tianjin Medical University. Patients were divided into two groups according to the location of the stones, and the related data were evaluated. In this study, 2485 unilateral and 1420 bilateral stone patients were included. Multivariate logistic regression analysis showed that BMI, gout, hyperparathyroidism, uric acid stone, urine PH, 24-h urinary calcium, blood uric acid, and metabolic syndrome (Mets) were independent risk factors for bilateral stone formation(P < 0.05). Based on these results, we construct a discrimination model. This model revealed good discrimination with an area under the receiver operating characteristic curves of 0.617, and the sensitivity and specificity were 0.592 and 0.586, respectively. Furthermore, the number of Mets components increased the risk of bilateral upper urinary tract stones. Hypertension, hyperglycemia, and low HDL level were strongly associated with bilateral upper urinary tract stones (P < 0.05). Patients with 5 components Mets had 1.89-fold higher risk of bilateral upper urinary tract stones than those with 1 component Mets (OR 3.381; 95 % CI 1.221-9.360; P = 0.013). Additionally, male patients with Mets had higher risk of bilateral upper urinary tract stones than female patients. Our analysis revealed that eight clinical factors were associated with the formation of bilateral upper urinary tract stones, namely BMI, gout, hyperparathyroidism, uric acid stone, urine PH, 24-h urinary calcium, blood uric acid, and Mets. This study could help clinicians adjust treatment strategies for high-risk patients with bilateral upper urinary tract stones.© 2024 The Authors.