Three-dimensional organic-inorganic hybrid perovskites (OHPs) hold a great prospect for photovoltaic applications due to their outstanding electronic and optical properties. These fascinating properties of OHPs in combination with their scalable and low-cost production make OHPs promising candidates for next-generation optoelectronic devices. The ability to obtain atomistic insights into physicochemical properties of this class of materials is crucial for the future development of this field. Recent advances in various scanning probe microscopy techniques have demonstrated their extraordinary capability in real-space imaging and spectroscopic measurements of the structural and electronic properties of OHPs with atomic-precision. Moreover, these techniques can be combined with light illumination to probe the structural and optoelectronic properties of OHPs close to the real device operation conditions. The primary focus of this review is to summarize the recent progress in atomic-scale studies of OHPs towards a deep understanding of the phenomena discovered in OHPs and OHP-based optoelectronic devices.