Objectives: The objective of this work is to investigate the impact of the pelvicalyceal anatomical system (PCS) on calyceal stone formation and surgical outcomes of endoscopic combined intrarenal surgery (ECIRS) for renal and/or proximal ureteral stones with a diameter >15 mm. Patients and methods: PCS was classified as Type I (single pelvis) or Type II (divided pelvis) according to the simple anatomical Takazawa classification. Using prospectively collected data from January 2016 to April 2020, 219 patients were retrospectively reviewed. After excluding patients who underwent a staged procedure, had hydronephrosis greater than grade 2, prior nephrostomy tubes, and failed to access the renal collecting system, 115 patients (Type I: 81, Type II: 34) were included, and the distribution of calyceal stones and surgical outcomes in ECIRS were compared between Types I and II PCS. Results: The median number of renal stone calyces in the Type II group was significantly more than that in the Type I group (p = 0.016). In particular, the Type II group possessed more upper stone calyces. Multivariate logistic regression analysis revealed that Type II PCS was associated with an increased odds ratio (OR) for the presence of upper stone calyces (OR: 2.93, p = 0.018). The stone-free (SF) status at 1 month after surgery, confirmed by abdominal plain radiography, was significantly higher in the Type I group compared with that in Type II (67.9% vs. 39.4%, respectively; p = 0.006). The requirement for additional surgical interventions was significantly higher in the Type II group compared with that in Type I (35.4% vs. 7.4%, respectively; p < 0.001). Multivariate analysis revealed that the number of stone calyces (OR: 4.26; p = 0.001) and Type II PCS (OR: 3.43; p = 0.009) were independent predictors of residual stones after ECIRS. Conclusion: We first revealed that the anatomic properties of PCS play a role in both upper calyceal stone formation and in the success of the ECIRS procedure. Because the SF rate in Type II PCS was significantly lower than that in Type I PCS, additional percutaneous nephrolithotomy tracts might be required, even for ECIRS.