Objective To report a case of urethral stricture, bladder stones and right ureteral stones in a patient with bilateral lower limb paralysis treated with innovative ureteral flexible endoscopic lithotripsy through cystostomy, so as to provide a new therapeutic approach for such complex cases.Case Report The patient, a 63-year-old male, was admitted due to fever for 45 days.He had been paraplegic in both lower limbs for 19 years and underwent cystostomy 2 years ago at another hospital. Abdominal computed tomography (CT) revealed right ureteral calculi complicated with multiple bladder stones.After adequate anti-infective therapy, cystoscopy was performed, during which complete posterior urethral atresia was identified.A flexible ureteral lithotripsy via the cystostomy site was successfully completed, with favorable therapeutic outcomes.On day 23 postoperatively, a follow-up plain radiograph of the urinary tract showed that the ureteral stent was in good position, with only a small number of residual stones in the prostatic fossa and no other stone remnants.Conclusion This provides a novel minimally invasive treatment approach for ureteral stones in patients who cannot undergo ureteroscopic intervention.