Fluorescence imaging has emerged as a widely adopted technique for in vivo biological studies due to its noninvasive nature, high specificity, and exceptional spatiotemporal resolution. Super-resolution microscopy transcends the diffraction limit, achieving spatial resolutions of tens of nanometers or better, enabling visualization of intricate intracellular structural changes. These methodologies demonstrate significant potential for examining the living brain, particularly in studying neuronal activities. This review examines recent developments in stimulated emission depletion microscopy (STED), structured illumination microscopy (SIM), single-molecule localization microscopy (SMLM), and super-resolution optical fluctuation imaging (SOFI) for in vivo imaging, addressing key challenges including imaging depth, phototoxicity, motion artefacts and three-dimensional reconstruction, while exploring imaging quality enhancement strategies such as multi-photon excitation, near-infrared imaging, adaptive optics, and deep-learning-based approaches. Additionally, it presents insights into the future trajectory of in vivo super-resolution imaging in neuroscience and clinical diagnostics.