Objective This project aims to investigate the diagnostic value of anti-Ro-52, anti-CENP-B, and AMA in Sjogren's syndrome and systemic sclerosis. Methods We constructed the Meta-analysis to evaluate the existing experimental data and obtain the advantages of the three antinuclear antibodies compared with traditional test items using specific data processing methods and evaluated their value in the diagnosis as well as the differential diagnosis of Sjogren's syndrome and systemic sclerosis. During the process of paper collection, we strictly followed the principle of PICOS to screen the literature, trying to include the literature with a large sample size, controversial and influential results which would make the results of this Meta-analysis more valuable. In this study, Revman and Stata software was used for data processing, and the forest map was drawn to analyze the difference in antibody-positive rate, age, and gender distribution, and other factors. At the same time, a funnel plot was used to evaluate the bias of literature results.Results The positive rate of anti-Ro-52 in SS and SSC was higher than that of anti-SSB (P < 0.00001); The positive rate of anti-CENP-B in SSc patients was higher than that in anti-SSB patients (P < 0.00001), but there was no significant difference in SS patients (P = 0.77); The positive rate of AMA in SS and SSc was significantly lower than that in ANA (P < 0.00001), but the expression of AMA increased in SS patients with autoimmune hepatitis. In patients with anti-Ro-52 positive SS and SSc associated with EBV infection, the former had a significantly increased risk of developing malignant lymphoma, while the latter had more severe symptoms of tissue fibrosis. Conclusion The accuracy of anti-Ro-52 in the diagnosis of SS and SSC is higher. The positive rate of anti-CENP-B in the diagnosis of SSc is higher than that of anti-SSB and anti-Scl-70. SS patients with EBV infection are more likely to develop into malignant lymphoma, while SSc patients with EBV infection have increased skin fibrosis and inflammation.