Objective To investigate the clinical value of intraoperative frozen section and paraffin section pathological diagnosis of breast tumors. Methods A total of 86 patients with breast tumors who were treated in our hospital from January 2022 to December 2023 were selected as the research objects. All patients underwent intraoperative frozen section diagnosis and paraffin section diagnosis. The time spent on the two diagnostic methods was compared and the diagnostic results were analyzed. Results The diagnostic time of paraffin section was longer than that of intraoperative frozen section (P <0.05). The diagnostic accuracy of tumor tissue ≤3 cm diagnosed by intraoperative frozen section was 86.15%, and the diagnostic accuracy of tumor tissue >3 cm was 90.48%. Compared with paraffin section diagnosis, the total complete coincidence rate of intraoperative frozen section diagnosis for breast tumor types was 90.70%, of which the complete coincidence rate for breast invasive carcinoma and breast fibroadenoma was 100.00%, followed by intraductal papilloma (91.67%), breast cystic hyperplasia (88.89%), breast invasive lobular carcinoma (84.21%), breast intraductal carcinoma (75.00%), breast phyllodes tumor (60.00%); the basic coincidence rate, false negative rate and delayed diagnosis rate of tumor types were 5.81%, 1.16% and 2.33%, respectively. There was no significant difference in the detection rate of tumor malignancy between intraoperative frozen section diagnosis and paraffin section diagnosis (P >0.05). The scores of intraoperative frozen section diagnosis on clarity, tissue morphology and tissue structure technology were higher than those of paraffin section diagnosis (P<0.05). Conclusion The accuracy of intraoperative frozen section in breast tumor diagnosis is similar to that of paraffin section, but the former diagnosis speed is faster and the section quality is higher, which is convenient for timely targeted treatment and promotes the improvement of the prognosis of patients. However, if there is any doubt in the diagnosis process, the comprehensive consideration should be combined with the pathological diagnosis results of paraffin sections, and then further treatment plan should be taken.