With the progress of science, the research objects of life science change from single organ to tissue, in vitro tissue slice, and live embryonic during development. The appearance of fluorescent-specific markers provides a means for tracking the process of the substance transfer within a single cell, tissue, organ, and even the entire embryo. In order to track the whole process, it is necessary to make nondestructive, non-invasive imaging of living embryos with sub-cellular level resolution, which poses higher requirements for fluorescence microscopy. We develop light-sheet fluorescence microscope and super-resolution fluorescence microscopy on the basis of traditional fluorescence microscopy. Light-sheet fluorescence microscope only excites the sample near the objective′s focal plane. Because of its high penetration depth, low photo-toxicity and photobleaching, and high imaging speed, light-sheet fluorescence microscope can be widely used in three-dimensional in vivo large scale biological imaging. Super-resolution fluorescence microscopy uses special light control means to improve the resolution of the microscope to nanometer level, which becomes a powerful weapon for exploring sub-cellular life activities. We introduce the development, integration, and the current problems encountered in the two technologies, and try to explore an imaging technique suitable for observing the subcellular structure and life process of three-dimensional large scale′s samples.