Objective  To use a new and improved S.T.O.N.E. stone scoring system to predict stone-free rate after stage Ⅰ retrograde intrarenal surgery (RIRS). The clinical data of 98 cases of patients with upper urinary calculi who underwent surgery by the same operator in our hospital from January 2020 to April 2021 were retrospectively analyzed. The correlation between the new modified S.T.O.N.E. stone scoring system and the stone-free rate after stage Ⅰ RIRS was analyzed. Results  All the 98 patients successfully completed the first stage of RIRS, and the overall one-time lithoclastic rate was 79.59% (78/98). The total scores of the new modified S.T.O.N.E. stone scoring system were 5-9 points, 10-12 points and 13-16 points, and the stone-free rates were 92.73% (51/55), 67.65% (23/34) and 44.44% (4/9), and the difference was statistically significant (P<0.001). The area under the curve (AUC) of the new modified S.T.O.N.E. stone scoring system was 0.781 (95%CI: 0.708-0.854), which was higher than that of any single variable, and the difference was statistically significant (P<0.05). The new modified S.T.O.N.E. stone grading system was compared with the original S.T.O.N.E. stone grading system. There was statistically significant difference  in stone scoring system between the two groups (P=0.015). Conclusions  The new modified S.T.O.N.E. stone scoring system can effectively predict the stone-free rate after stage Ⅰ RIRS.