Objective To analyze the relationship between the expression of carbonic anhydrase 3 (CA3) in breast cancer tissues, its prognostic potential and the number of immune cells by a variety of online databases. Methods GEPIA2.0 and TIMER databases were used to analyze the difference of CA3 mRNA expression in breast cancer tissues. Bc-GenExMinerv4.7 database was used to analyze the difference of CA3 mRNA expression in breast cancer subcategories. Kaplan-Meier plotter, Bc-GenExMinerv4.7 and PrognoScan databases were used to analyze the effect of CA3 mRNA expression levels on prognosis of patient. LinkedOmics database was used to analyze of the biological behavior involved in CA3 co-expressed genes. TIMER database was used to analyze the relationship between CA3 mRNA expression and immune cells infiltration in breast cancer tissues. Results The expression of CA3 mRNA in breast cancer tissues was lower than that in normal breast tissues (P<0.05), and the expression levels of CA3 mRNA were higher in ER negative (P<0.05), PR negative (P<0.05), HER2 negative (P<0.05) and no lymphatic metastasis (P<0.05). In addition, the expression level of CA3 in breast cancer patients with high Ki67 expression was lower (P<0.05) and closely related to SBR and NPI grade (P<0.05). Breast cancer patients with low expression of CA3 mRNA had lower overall survivall, recurrence free survival, and disease free survival ( P<0.05). Ten of the top 50 positively correlated co-expressed genes screened out had low risk ratio (P<0.05), and 11 of the top 50 negatively correlated co-expressed genes screened out had high risk ratio (P<0.05). The expression of CA3 mRNA was positively correlated with CD4+ T cells and CD8+ T cells in breast cancer tissues (rs=0.175, P<0.001; rs=0.137, P<0.001), and negatively correlated with T cell failure markers LAG3, TIM-3 and PVRL2 (rs=–0.100, P<0.01; rs=–0.143, P<0.001; rs=–0.082, P<0.05). Conclusions The low expression of CA3 mRNA in breast cancer tissues is correlated with the occurrence, development and prognosis of breast cancer. CA3 can be used as a potential independent prognostic marker for breast cancer and may be related to immune infiltration.