Objective To explore the application of single-disease modular teaching in the standardized training of resident physicians in urology (referred to as residency training). Methods A controlled trial was conducted. Through consecutive sampling, 84 residents rotating in the Department of Urology, the Second Hospital of Tianjin Medical University enrolled in the study. Among them, 44 residents in 2022 were assigned to the experimental group, receiving single-disease modular teaching; 40 residents in 2021 served as the control group, undergoing traditional teaching. One month after training, the training effect was evaluated through knowledge examinations, clinical skills and clinical thinking assessments, and questionnaires. Independent sample t-test and χ² test were used for data analysis. Results The experimental group showed significantly higher scores than the control group in knowledge examination [(87.66±4.47) vs. (81.78±5.61)] and clinical skills assessment [(88.95±3.63) vs. (80.18±4.62)] (all P<0.05). In terms of medical record writing standardization [(88.80±3.42) vs. (82.88±4.01)], clinical thinking ability [(88.39±3.61) vs. (81.65±4.69)], and doctor-patient communication skills [(16.30±2.12) vs. (13.93±1.86)], the experimental group also achieved significantly higher scores (all P<0.001). Teaching satisfaction survey showed that the experimental group scored higher in all dimensions: practicality of teaching content [(4.52±0.59) vs. (3.95±0.50)], teaching ability of instructors [(4.50±0.59) vs. (3.80±0.56)], diversity of teaching methods [(4.48±0.55) vs. (3.65±0.58)], stimulation of learning interest [(4.52±0.51) vs. (3.80±0.52)], improvement of autonomous learning ability [(4.16±0.37) vs. (3.68±0.53)], mastery of clinical skills [(4.07±0.26) vs. (3.63±0.49)], standardization of medical record writing [(4.02±0.34) vs. (3.75±0.44)], enhancement of clinical thinking [(4.07±0.40) vs. (3.55±0.60)], improvement of doctor-patient communication [(4.11±0.44) vs. (3.75±0.59)], and overall satisfaction [(4.18±0.50) vs. (3.88±0.52)] (all P<0.05). Additionally, the comprehensive evaluation of the experimental group by instructors was significantly higher than the control group [(91.48±3.23) vs. (85.83±3.73)] , and the difference was statistically significant (P<0.001). Conclusions Single-disease modular teaching helps urology residents understand and master theoretical knowledge, and improves their clinical skills, clinical thinking, and teaching satisfaction.