Controlled synthesis of nanostructure ultrathin films is critical for applications in nanoelectronics, photonics, and energy generation and storage. The paucity of structural probes that are sensitive to nanometer-thick films and also capable of in-operando conditions with high spatiotemporal resolutions limits the understanding of morphology and dynamics in ultrathin films. Similar to X-ray fluorescence holography for crystals, where holograms are formed through the interference between the reference and the object waves, we demonstrated that an ultrathin film, being an X-ray waveguide, can also generate fluorescence holograms as a result of the establishment of X-ray standing waves. Coupled with model-independent reconstruction algorithms based on rigorous dynamical scattering theories, the thin-filmbased X-ray waveguide fluorescence holography becomes a unique in situ and time-resolved imaging probe capable of elucidating the real-time nanostructure kinetics with unprecedented resolutions. Combined with chemical sensitive spectroscopic analysis, the reconstruction can yield element-specific morphology of embedding nanostructures in ultrathin films.