Retrograde intrarenal surgery (RIRS) and percutaneous nephrolithotomy (PCNL) are both important minimally invasive techniques for the treatment of renal stones. With the progress of technology, the application of procedures has been extended. Current surgery choices are made base on stone size, burden and its locations that might limit the predictability and removal of post-operative residual stones. Despite these surgery techniques are maturely used in clinical practice, the patients’ selection have not been standardized in borderline stone. Some patients might suffer several sessions of surgery if intervene decision are not well-designed. In this single-center study, we aimed to determine whether the Hounsfield Unit (HU) value of no-contrast computer computed tomography (NCCT) might offer better guidance in the selection of RIRS or PCNL in renal stones of 2-3 cm, not only in facilitating the stone disintegration, also in providing the potential optimal and less session of setting with great outcomes. A total of 158 patients with kidney stones (2-3 cm) who underwent PCNL/RIRS from March 2016 to January 2019 were enrolled in this study. Gender, stone sizes, locations, average HU value of stone, surgery time, hospital stay time, stone free rate and complications at the time of hospitalization and 3 month follow-up were measured to identify the surgery efficiency. Upon consideration of HU value, the mean surgery time were significantly decreased in RIRS comparing to cRIRS group (47.73 ± 15.52 versus 72.41 ± 27.71 min, p<0.05). Statistically, the surgery time was strong influenced by the HU values both in RIRS (OR: 93.8, p<0.01) and PCNL (OR, 8.21, p<0.05). HU values proved to have a strong positive relation with surgery time in RIRS while a low positive related in PCNL (p<0.05). Overall, for renal stones of 2-3 cm, RIRS proved to be a safe and efficacious treatment option if HU value and other parameters could be comprehensively accounted. Considering HU value before 2-3cm kidney stone lithotripsy seems to be necessary, which might save the surgery time and reduce the potential risk of renal injury, as even if residual stone were detected post-op, ESWL could also be employed and work efficiently. Some patients might not have to perform several sessions of RIRS. Taken together, individual precision surgery might provide ideal treatment and prognosis for patients requiring long-term continuous clinical procedures.