Small fluorescent molecules have been an important tool for fluorescence-based imaging, thanks to their technical simplicity, sensitivity and structural flexibility. However, probing specific intracellular systems with a small fluorescent molecule is not an easy task owing to the intricate nature of the cells. Ideal imaging probes should be highly permeable and be without background noise to allow undisrupted observations. These probes will unquestionably be more advantageous for interrogating intracellular architectures and dynamics without compromising the cellular integrity, and could therefore be applied for applications in the native cellular environment. This review will highlight the advances in design strategies for cell-permeable fluorescent probes through a diversity-oriented fluorescence library approach and rational design via computational-aided predictive models. Here, we discuss a series of cell-permeable probe applications for imaging specific cell types and intracellular biomolecules, as well as the cellular environment.