The objectives of the study are to compare the safety and efficacy of all-seeing needle optical puncture system micro-percutaneous nephrolithotomy (micro-PCNL) and flexible ureterorenoscopy (FURS) for the treatment of lower calyceal stones of 2cm and to determine the advantages and disadvantages of each. 116 patients in total with lower calyceal stones of 2cm were randomly divided into two equal groups, all-seeing needle optical puncture system micro-PCNL and FURS. In both groups, holmium laser was utilized for lithotripsy. The perioperative parameters were compared between the two groups. Compared to the all-seeing needle micro-PCNL group, the mean operative time was significantly longer in the FURS group (P=0.000). However, there was no significant difference between the two groups with respect to mean hemoglobin reduction (P=0.087), complications (P=0.731) and LOS (P=0.856). The overall SFR of the all-seeing needle micro-PCNL group and FURS group was 84.5% (49/58) and 79.3% (46/58), respectively, without any significant difference between the groups (P=0.469). For treating lower calyceal stones of 2cm, the all-seeing needle micro-PCNL group had shorter operative time than FURS, while no significant differences between the two groups with respect to mean hemoglobin reduction, complications, LOS and SFR were found.