Cell-to-cell communication plays an important role in development, reproduction, and environmental responses by coordinating the cell activity in multicellular organisms. In plant development, cell-to-cell communication is especially crucial because organogenesis is a postembryonic and continuous process. However, it is difficult to reveal the dynamics of intercellular communications due to the limitation of accessibility within several cell layers in plants. Recently, two-photon excitation microscopy with near-infrared femtosecond pulse laser provides a non-invasive tool for deep imaging. In this review, we discuss recent deep imaging containing the preparation of specimens and microscopic techniques. Moreover, optical manipulation technique with near-infrared ultrafast pulse laser enables us to disrupt the cell and the protein at the single-cell level. Combination of in vivo deep imaging and optical manipulation, which allow spatial and temporal control of cell activity, provides a new view of the cell-to-cell communication in plant field.