The correlation between novel negative pressure ureteroscopic lithotripsy (NP-URL) combined with flexible ureteroscopy (FU) and percutaneous nephrolithotomy (PCNL) on stone-free rates (SFR) remains unclear. There is a lack of evidence from Chinese populations regarding the relationship between SFR and NP-URL combined with FU (NP-URL-FU) versus PCNL. We aimed to assess the association between NP-URL-FU and PCNL on SFR. We conducted a cohort study involving 166 participants with 2–4 cm kidney stones. Data on SFR (7 days and 2 months) were collected from all participants. Logistic regression analysis was used to substantiate the research objectives. NP-URL-FU versus PCNL showed an 86% decrease in the 7-day SFR (OR = 0.14, 95% CI 0.07–0.29). The results remained stable even after adjusting for potential confounders. However, no statistically significant association was found between the surgical method and the 2-month SFR. Further exploratory subgroup analyses showed no significant interactions, with all P values > 0.05. Among patients with 2–4 cm kidney stones, NP-URL-FU was associated with a lower risk of incident 7-day SFR than PCNL. However, no statistically significant difference was found in the long-term stone removal rate. Therefore, NP-URL-FU may be a viable alternative surgical option for patients seeking minimally invasive procedures.