Bilateral upper urinary tract stones are more likely to lead to impairment of renal function, but few biochemical metabolic studies of bilateral upper urinary tract stones have been reported. We collected clinical data from 555 patients with upper urinary tract stones admitted to Beijing Tsinghua Changgung Hospital from June 2020 to June 2024, and divided them into unilateral and bilateral stone groups by CT scans, analysed the metabolic differences between unilateral and bilateral stone groups by statistical methods, and used multifactorial logistic regression analysis to explore the risk factors that might affect the formation of bilateral stones. A total of 281 cases of unilateral and 274 cases of bilateral stones were identified. The proportion of male patients in the bilateral group was higher than that in the unilateral group (P < 0.05). The most prevalent major stone component was calcium oxalate monohydrate (48.1%), with a significantly higher prevalence of cystine stones observed in the bilateral stone group (1.8%) compared to the unilateral stone group (0.4%) (P < 0.05). Blood uric acid, blood BUN, blood creatinine, urine pH, and 24-hour urine output were higher in the bilateral stone group than in the unilateral group (P < 0.05). The most prevalent metabolic abnormality was low urine volume (45.7%). Bilateral stone group had higher proportion of patients with hyperuricemia (P < 0.05). The results of the multivariate logistic regression analysis showed that male gender (OR 1.489, 95% CI 1.028–2.157) and hyperuricemia (OR 1.662, 95% CI 1.113–2.482) were associated with an increased risk of bilateral stone formation (P < 0.05). There are significant differences in biochemical metabolism between unilateral and bilateral upper urinary tract stones. The most common metabolic abnormality in patients with urolithiasis is low urine output, and aggressive water intake is effective in preventing stone formation. For patients with hyperuricemia, a strict dietary regimen is imperative to mitigate the likelihood of bilateral stone formation.