Background: Non-muscle invasive bladder cancer (NMIBC) has a high recurrence and progression rate, and the intravesical instillation chemotherapy drugs is diverse. To optimize patient prognosis, patient-derived tumor-like cell clusters (PTC) for drug testing seeks to identify an effective drug for individual patient. Methods: A prospective, single-center, parallel-group, randomized phase II clinical trial was conducted from December 2020 to December 2023 in Department of Urology of the Second Hospital of Tianjin Medical University (ClinicalTrials.gov: ChiCTR2000040996). This study enrolled a total of 120 patients who had been diagnosed as NMIBC. Patients who met the inclusion and exclusion criteria were randomly assigned to either the control group or the PTC drug-screening group. In the control group, chemotherapy drugs (gemcitabine, pirarubicin, epirubicin and hydroxycamptothecin) were selected for intravesical instillation according to the doctor's experience. In the PTC group, chemotherapy drugs were administered according to PTC drug screening results. Results: The PTC group was associated with significantly lower 1-year Relapse-Free Survival (RFS) rate (10.0 %; 95% CI, 2.4%-17.6%,) compared with the control (31.7%; 95% CI, 19.9%-43.4%), (HR=0.2264; 95% CI, 0.0845-0.6068; p = 0.0013). Similarly, the PTC group was associated with significantly lower 2-year RFS rate (18.3%; 95% CI, 8.5%-28.1%) compared with the control (48.3%; 95% CI, 35.7%-61.0%), (HR=0.3730; 95% CI, 0.1756-0.792; p = 0.0075). Conclusions: PTC drug screening significantly reduced the recurrence rate of postoperative NMIBC. Clinical trial information: ChiCTR2000040996.