Purpose To evaluate the Metabolic syndrome(MetS) in patients with unilateral and bilateral staghorn calculus(SC) and compare the impact on the outcome of percutaneous nephrolithotomy(PCNL).Methods The patients who underwent PCNL for the treatment of SC were retrospectively reviewed between 2019–2022. SC were divided into unilateral and bilateral. The variables of the patients were calculated to evaluate the MetS difference between unilateral and bilateral SC and the impact on the outcome of PCNL.Results 1778 patients were received PCNL between 2019 and 2022, After screening computed tomography, A total of 379 patients with staghorn calculus, patients without follow-up and incomplete data were excluded, finaly 310 patients with SC were included. 84 with bilateral SC and 226 with unilateral. More higher body mass index, complete staghorn and metabolic syndrome were found in the patients with bilateral SC. Higher body mass index, hypertension, diabetes mellitus, hyperlipidemia, MetS were 62.58%, 44.84%, 21.94%, 60.65% and 27.42% in patients. 85 patients with MetS(+) resulted in higher rate of overall complication(Number(N)(%), 29(38.10) VS 54(23.89), p = 0.013) and comparable stone free rate with 225 MetS(-). Multivariable analysis confirmed that hyperlipidemia(p = 0.044, odds ratio[OR] = 1.991, 95% confidence interval[CI] 1.020–3.888) and MetS ( p = 0.005, OR = 2.427, 95%CI 1.316–4.477) were independent risk factors for overall complication.Conclusions MetS are strongly correlated with the formation of bilateral SC and is the core predictor in assessing overall complication for PCNL.