To investigate the diagnostic value of intraoperative cytology and rapid immunocytochemistry in primary central nervous system lymphoma. 254 cases of lymphoma and 82 cases of non-lymphoma were collected from 2010 to 2023. Frozen section(FS) was using alone in 44 cases during 2010–2014, FS and intraoperative cytology(IC) were using in 251 cases during 2015 to 2022. Rapid immunocytochemical(RICC, CD20, GFAP) were using with FS + IC in 41 cases during 2021 to 2023. Method One: According to the results of archives, statistic the diagnostic accuracy of lymphoma during three time periods. Method Two: All cases were randomly renumbered, 4 neuropathologists compared the accuracy of independent histology and that of combining cytology. The archives showed the diagnostic accuracy of FS in PCNSL was 77.27%, FS + IC was 86.06%, FS + IC + RICC was 92.68%. The retrospective study demonstrated the diagnostic accuracy of FS was 79.76%, FS + IC was 87.33% and FS + IC + RICC was 92.68%. The positive predictive value, negative predictive value, sensitivity, specificity and accuracy of CD20 were 100%, 76.92%, 90.32%, 100% and 92.68%, respectively. The results of the paired χ2 test was no statistically significant difference (0.05 < P < 0.1) between FS + IC + RICC and immunohistochemical (IHC) diagnosis of paraffin sections. The integration of IC + RICC + FS diagnosis can significantly enhance the intraoperative diagnostic accuracy of PCNSL and rectify potential errors that may occurred when relying solely on FS diagnosis.