Objective To identify the immune responses induced by subunit vaccine of Ag85B-ESAT-6 (AE) fusion protein by mucosal route and the protection against Mycobacterium tuberculosis (MTB) infection in mice. Methods AE and AE with c-di-AMP as adjuvant were inoculated intranasally in mice. The generation of specific IgG, cytokines secreted by Th1 cells (IFN-γ, IL-2) and Th2 cells (IL-10) were detected by ELISA. The transcriptional levels of IFN-γ, IL-2, IL-10, and TNF-α were determined using real-time quantitative PCR. After MTB infection by vein, the antibodies level in mice sera and cytokines secretion of splenocytes were detected by ELISA. Histopathological changes in mice lung was illustrated by HE staining, and bacteria burdens of spleen and lung were counted by colony-forming units (CFUs) on plate. Results AE and AE combined with c-di-AMP via nasal mucosal immunization could induce high level specific antibodies in sera, promote splenocyte proliferation, and lead to increased Th1/Th2 cytokines and TNF-α transcription in spleen and lung, and secret more Th1/Th2 cytokines in spleen. After MTB infection, compared with the control group, the specific antibody levels of AE and AE combined with c-di-AMP immunized mice still increased, with enhanced the Th1/Th2 cellular immune responses, inflammatory response in the lung tissues, and reduced bacteria loads in spleen and lung, especially in mice immunized with AE combined with c-di-AMP. Conclusion Intranasal mucosal vaccination of AE subunit vaccine can induce humoral and cellular immune responses, and provide protection against MTB infection in mice, c-di-AMP as an adjuvant can improve the immunogenicity of AE to a certain extent.