Background: To explore and analyse the curative effects of a holmium laser under a flexible ureteroscope in the treatment of endogenous renal cysts complicated with renal calculi. Methods: Seven patients with endogenous renal cysts and renal calculi were admitted to our hospital from April 2019 to April 2021. The renal calculi was smashed by a holmium laser under a flexible ureteroscope, and the kidney cysts were opened by holmium laser endotomy. Window decompression was performed, indwelling the ureteral double-J tube for 1 month after the operation. After 1 month, when the patient was hospitalized and the double-J tube was removed, a flexible ureteroscope was inserted into the renal pelvis to confirm the effect of window opening and lithotripsy, and CT or B-ultrasound was reviewed. Results: Among the 7 patients with endogenous renal cysts and kidney stones, one patient was scheduled to undergo an internal incision after successful lithotripsy. The renal cyst wall tissue was surrounded by the renal artery, and the internal incision was terminated. One patient had an unsuccessful lithotripsy due to the poor angle of the kidney stone but was successfully treated for the renal cyst. The remaining 5 patients successfully underwent lithotripsy and internal incision surgery, of which 2 cases had difficulty finding kidney cysts and stones during the operation and needed assistance in locating kidney cysts and kidney stones under B-ultrasound monitoring. The average operation time was 42 minutes. When the catheter was extubated, the diameter of the renal cyst window was 0.5 cm to 2.5 cm under a flexible ureteroscope. The stone discharge was fair. There were residual gravels in the lower calyx of the kidney in two patients, and the stone basket was removed. After extubation, the maximum diameter of the renal cyst was reduced by more than half by CT or B-ultrasound, the effect of fenestration and decompression was achieved, and there were no obvious residual stones. Conclusions: A holmium laser under a flexible ureteroscope has a reliable curative effect in the simultaneous treatment of endogenous renal cysts with kidney stones, with little damage, quick recovery, and low cost. It can be used as the first choice for the treatment of endogenous renal cysts with kidney stones.