Objective To explore the application value of MSCT 3D reconstruction technique in flexible ureteroscopy and holium laser lithotripsy (FURL) for subrenal calyx calculus. Methods Data of 67 subrenal calyx calculus patients treated with FURL were analyzed retrospectively. The anatomic difference between surgically cured group and uncured one was compared by measuring the renal pelvis subrenal calyx infundibulopelvic angle (IPA), the calyx width and length, as well as the minimum ratio of subrenal calyx neck width and calyx transverse diameter (minN/T) with MSCT 3D reconstruction technique. The anatomic structure factors that may impact the operative success rate were discussed. Results Among the 67 patients, 52 patients were cured and in cured group, and 15 patients were in uncured group. The average IPA value in cured group was significantly higher than that in uncured group:(54.12 ± 21.32)° vs. (42.12 ± 22.68)° , and there was significantly difference (P<0.05). Twenty-six patients performed CT 3D reconstruction and IVU examination at the same time. The level of IPA in CT 3D reconstruction was significantly higher than that in IVU examination : (53.12 ± 10.16)° vs. (47.67 ± 11.25)° , and there was significant difference (t=1.676, P<0.05). Logistic regression analysis showed that IPA and minN/T levels were the influencing factors of FURL for subrenal calyx calculus. Conclusions The MSCT 3D reconstruction technique can better describe the anatomical relationship of the subrenal calyx. The success rate of FURL relates to the IPA value and the min N/T, which is significant in preoperative indication evaluation.