The technological development in modern optical imaging and fluorescent labeling has provided important tools for obtaining high-resolution three-dimensional (3D) structural information about biological tissues. However, the opaque nature of most biological tissues limits the light penetration depth, which limits their applications for large tissue specimens or organs. In recent years, optical clearing methods that employ various physical and chemical means have been proposed for reducing light attenuation and improving the imaging depth, thereby providing novel perspectives for 3D imaging of large samples or whole organs. This paper reviews the tissue optical clearing methods for imaging whole organs from three aspects: in vitro optical clearing methods for tissues, whole-mount labeling methods, and 3D imaging techniques.