ObjectiveTo　develop　a　multimodal　imaging　atlas　of　a　rat　brain-computer　interface　(BCI)　that　incorporates　brain,　arterial,　bone　tissue　and　a　BCI　device　using　mixed　reality　(MR)　for　three-dimensional　(3D)　visualization.MethodsAn　invasive　BCI　was　implanted　in　the　left　visual　cortex　of　4-week-old　Sprague-Dawley　rats.　Multimodal　imaging　techniques,　including　micro-CT　and　9.0　T　MRI,　were　used　to　acquire　images　of　the　rat　cranial　bone　structure,　vascular　distribution,　brain　tissue　functional　zones,　and　BCI　device　before　and　after　implantation.　Using　3D-slicer　software,　the　images　were　fused　through　spatial　transformations,　followed　by　image　segmentation　and　3D　model　reconstruction.　The　HoloLens　platform　was　employed　for　MR　visualization.ResultsThis　study　constructed　a　multimodal　imaging　atlas　for　rats　that　included　the　skull,　brain　tissue,　arterial　tissue,　and　BCI　device　coupled　with　MR　technology　to　create　an　interactive　3D　anatomical　model.ConclusionsThis　multimodal　3D　atlas　provides　an　objective　and　stable　reference　for　exploring　complex　relationships　between　brain　tissue　structure　and　function,　enhancing　the　understanding　of　the　operational　principles　of　BCIs.　This　is　the　first　multimodal　3D　imaging　atlas　related　to　a　BCI　created　using　Sprague-Dawley　rats.