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Endo‐microscopy is crucial for real‐time 3D visualization of internal tissues and subcellular structures. Conventional methods rely on axial movement of optical components for precise focus adjustment, limiting miniaturization and complicating procedures. Meta‐device, composed of artificial nanostructures, is an emerging optical flat device that can freely manipulate the phase and amplitude of light. Here, an intelligent fluorescence endo‐microscope is developed based on varifocal meta‐lens and deep learning (DL). The breakthrough enables in vivo 3D imaging of mouse brains, where varifocal meta‐lens focal length adjusts through relative rotation angle. The system offers key advantages such as invariant magnification, a large field‐of‐view, and optical sectioning at a maximum focal length tuning range of ≈2 mm with 3 µm lateral resolution. Using a DL network, image acquisition time and system complexity are significantly reduced, and in vivo high‐resolution brain images of detailed vessels and surrounding perivascular space are clearly observed within 0.1 s (≈50 times faster). The approach will benefit various surgical procedures, such as gastrointestinal biopsies, neural imaging, brain surgery, etc. [ABSTRACT FROM AUTHOR]